SARS-CoV-1 Infection (Homo sapiens)

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membrane vesicle viral factory outer membranepp1a-nsp10 m7G(5')pppAm-capped,polyadenylated mRNA5ACE2 inhibitorspp1ab-nsp6 PPiSUMO-p-Ncap dimerpp1ab-nsp16 SARS-CoV-1 minusstrand subgenomicmRNAsUb-3xPalmC-E pp1ab-nsp10 N-glycan pp1a-nsp3 pp1a-nsp10 M pp1ab-nsp4 pp1ab-nsp8 RB1SUMO-p-Ncapdimer:SARScoronavirus genomicRNAUb-3xPalmC-E pp1ab-nsp12 RPS27A(1-76) RB1 pp1ab-nsp16Ub-3xPalmC-Epentamerpp1ab-nsp14 complex N-glycan-PALM-Spike pp1ab-nsp3 SARS coronavirusgRNA:RTC:nascentRNA minus strandwith mismatchednucleotidetrimmedN-glycan-PALM-Spiketrimerp-S177-Ncappp1ab-nsp6 H2Opp1a-nsp6 CQ, HCQnsp9 dimerpp1a-nsp3 H+O-glycosyl 3atetramerpp1a-nsp3 pp1a-nsp7 SARS coronavirus nascent genomic RNA complement (minus strand) with mismatched 3' nucleotide pp1ab-nsp12 3xPalmC-Em7G(5')pppAm-capped,polyadenylated mRNA3pp1ab-nsp7 pp1a-nsp10 M N-glycan M pp1a-nsp6 MSARS-CoV-1gRNA:RTC:nascentRNA minusstrand:RTCinhibitors3CLpdimer:α-KetoamidesS-adenosyl-L-methionineCTSL(292-333) MGAT1pp1ab-nsp6 ZCRB1:SARS-CoV-1genomic RNA (plusstrand)pp1a-nsp3-4 N-glycan M pp1ab-nsp7pp1ab-nsp8 pp1ab-nsp3 7a O-glycosyl 3a SUMO1:C93-UBE2INcapcomplex N-glycan-PALM-Spike NTPpp1ab-nsp10 pp1ab-nsp7 N-glycan M N-glycan MUBC(153-228) N-glycan pp1a-nsp4 pp1ab-nsp8 O-glycosyl 3a pp1a-nsp8 m7GpppA-capped SARS-CoV-1 genomic RNA (plus strand) pp1ab-nsp14 ER-alphaglucosidases:ER-alpha glucosidase inhibitorspp1a-nsp4 ST3GAL2 pp1ab-nsp12 H+glycosylated-ACE2pp1ab-nsp5pp1a-nsp9 M pp1ab-nsp9 trimmed N-glycanSpikeS3:M:E:encapsidatedSARS coronavirusgenomicRNA:7a:O-glycosyl3a tetramerpp1a-nsp6SUMO1-K62-ADPr-p-S177-Ncap M GSK3BH+3a:membranousstructureO-glycosyl 3a a nucleotide sugarST3GAL3 complexN-glycan-PALM-Spiketrimerpp1ab-nsp16 CMP-Neu5Ac3aN-glycan nsp3-4m7G(5')pppAm-mRNA5 pp1ab-nsp15 mRNA8 minus strand pp1ab-nsp6 m7G(5')pppAm-cappedSARS-CoV-1 genomicRNA complement(minus strand)mRNA3 nsp2pp1a-nsp7 pp1ab-nsp14 nsp10pp1ab-nsp15 pp1ab-nsp7 CMPpp1a-nsp1 pp1a-nsp3 m7G(5')pppAm-capped, polyadenylated SARS-CoV-1 genomic RNA (plus strand) UDPSUMO1-K62-ADPr-p-S177-Ncap pp1ab-nsp8 cepharanthine PARP6 Host Derived Lipid Bilayer Membrane pp1a-nsp10 PPipp1a-nsp8 CHMP4C pp1ab-nsp10 pp1ab-nsp6 m7GpppA-capped SARS-CoV-1 genomic RNA (plus strand) pp1a-nsp10 m7GpppA-mRNA6 pp1ab-nsp10 m7G(5')pppAm-capped, polyadenylated SARS-CoV-1 genomic RNA (plus strand) pp1ab-nsp6 pp1ab-nsp4 Ub-3xPalmC-E GSK3A UBC(305-380) pp1ab-nsp16 PARP14 Ub-3xPalmC-E pp1ab-nsp10 pp1a-nsp3 SUMO1-K62-ADPr-p-S177-Ncap ST6GALNAC4 pp1ab-nsp12 pp1ab-nsp7 CQ2+, HCQ2+complex N-glycan-PALM-Spike pp1ab-nsp8 pp1ab-nsp12 VHL pp1ab-nsp16 Ub-3xPalmC-E pp1ab-nsp16 m7G(5')pppAm-SARS-CoV-1 plus strand subgenomic mRNAspp1ab-nsp7 complex N-glycan-PALM-Spike S2 Fragment pp1a-nsp8 pp1ab-nsp6 pp1a dimercomplex N-glycan-PALM-Spike H+Ub7a SARS coronavirusgRNA:RTC:RNAprimer:RTCinhibitorspp1ab-nsp4 m7G(5')pppAm-capped,polyadenylated mRNA3 a nucleotide sugarRTC inhibitorsm7G(5')pppAm-mRNA2 beta-D-glucosepp1ab-nsp13 nsp16:VHLUBC(381-456) pp1a-nsp7 SUMO1-K62-p-S177-Ncap dimernsp4pp1ab-nsp10 nucleotide-sugarpp1ab-nsp14 ER-alpha-glucosidaseinhibitorspp1a-nsp6 pp1a-nsp4 Pipp1ab-nsp14 m7G(5')pppAm-capped, polyadenylated SARS-CoV-1 genomic RNA (plus strand) m7G(5')pppAm-mRNA7 PARPs7a trimmedN-glycan-PALM-Spiketrimerm7G(5')pppAm-capped,polyadenylated mRNA4 pp1ab-nsp10 BECN1 NTPpp1ab-nsp13 SARS-CoV-1 nascent genomic RNA complement (minus strand) complex N-glycan-PALM-Spike nucleoside5'-diphosphate(3−)pp1a-nsp6 mRNA3 minus strand S-adenosyl-L-homocysteinepp1a-nsp7 O-glycosyl 3a pp1ab-nsp1 pp1ab-nsp5 pp1ab-nsp8Ub-3xPalmC-E pp1a-nsp6 pp1a-nsp8 pp1a-nsp8 m7G(5')pppAm-capped SARS-CoV-1 genomic RNA complement (minus strand) glycosylated-ACE2 m7GpppA-mRNA9 m7GpppA-capped SARS-CoV-1 genomic RNA (plus strand) pp1ab-nsp12 pp1ab-nsp7 pp1ab-nsp10 pp1a-nsp6 pp1a-nsp10 pp1a-nsp7 mRNA6 7a TMPRSS2m7G(5')pppAm-capped,polyadenylatedSARS-CoV-1 genomicRNA (plus strand)PARP8 N-glycan M nsp8Ub-3xPalmC-E PPiCTSL:CTSL inhibitorsnsp7:nsp8:nsp12pp1ab-nsp6 N-glycan nsp3complex N-glycan-PALM-Spike S1 Fragment pp1ab-nsp13 SUMO1-K62-ADPr-p-S177-Ncappp1ab-nsp6m7G(5')pppAm-capped, polyadenylated SARS-CoV-1 genomic RNA (plus strand) pp1ab-nsp16 glycosylated-ACE2pp1ab-nsp4 pp1ab-nsp8 pp1ab-nsp4 H2OO-glycosyl 3atetramerpp1ab-nsp14 CHMP4B 7a H2OGalNAc-O-3aTMPRSS2 inhibitorspp1a-nsp8 pp1a-nsp8 M pp1ab-nsp10 m7G(5')pppAm-capped,polyadenylatedSARS-CoV-1 genomicRNA (plus strand)complex N-glycan-PALM-Spike S1 Fragment pp1ab-nsp16 N-glycan Epp1aN-glycanpp1ab-nsp3-4S3:M:E:encapsidatedSARScoronavirusgenomicRNA:7a:O-glycosyl3atetramer:glycosylated-ACE2pp1ab-nsp8 pp1ab-nsp8 pp1a-nsp8 Pipp1a-nsp4 pp1ab-nsp14 SARS-CoV-1 gRNAcomplement (minusstrand):RTC:RTCinhibitorsSUMO1-K62-p-S177-Ncap dimerUBB(153-228) pp1ab-nsp15 CTSL(114-288) 8b:MAP1LC3Bpp1ab-nsp6 nsp5pp1a-nsp3 SUMO1-C93-UBE2I pp1ab-nsp15 pp1ab-nsp3 pp1a-nsp8 SUMO1-K62-ADPr-p-S177-Ncap pp1ab-nsp14 pp1ab-nsp5 CHMP7 pp1a-nsp10 nsp13:DDX5PRKCSH UVRAG pp1ab-nsp14 pp1a-nsp9 pp1ab-nsp10 mRNA7 minus strand SARS-CoV-1 nascent genomic RNA complement (minus strand) nsp1-4Ub-3xPalmC-Enucleoside5'-diphosphate(3-)ST3GAL1 pp1ab-nsp10 pp1a-nsp6 pp1ab-nsp12 palmitoyl-CoAPARP4 pp1ab-nsp3 pp1ab-nsp10 pp1a-nsp7 pp1ab-nsp13 M m7GpppA-capped SARS-CoV-1 genomic RNA (plus strand) MOGS pp1a-nsp3 GSK3B:GSKim7GpppA-cappedSARS-CoV-1 genomicRNA complement(minus strand)CHMP2B S3:M:E:encapsidatedSARS coronavirusgenomicRNA:7a:O-glycosyl3a tetramerpp1ab-nsp2 pp1ab-nsp15 pp1a-nsp10 nsp15:RB1S1:S2:M:E:encapsidated SARS coronavirus genomic RNA: 7a:O-glycosyl 3a tetramerNmRNA5 minus strand mRNA4 pp1ab-nsp3 pp1ab-nsp13 pp1ab-nsp9pp1ab-nsp14NTPm7G(5')pppAm-capped SARS-CoV-1 genomic RNA complement (minus strand) encapsidated SARScoronavirus genomicRNApp1ab-nsp16 NAD+pp1a-nsp9sialyltransferasesnsp7:nsp8:nsp12:nsp14:nsp10:nsp13:nsp15m7GpppA-capped SARS-CoV-1 genomic RNA (plus strand) nsp7:nsp8pp1a-nsp7pp1ab-nsp7 GANAB pp1a-nsp7 O-glycosyl 3a H2Opp1ab-nsp7 pp1ab-nsp13 pp1a-nsp4 pp1a-nsp10 pp1a-nsp3 pp1a-nsp1-4 mRNA7 nsp3:nsp4:nsp6ST6GAL1 pp1a-nsp7 pp1a-nsp7 pp1a-nsp3 nsp3-4m7GpppA-mRNA5 N-glycan pp1ab-nsp4 pp1ab-nsp1-4 ST6GALNAC3 mRNA2 pp1ab-nsp7 O-glycosyl 3a pp1ab-nsp4 pp1ab-nsp13 H+m7GpppA-mRNA4 pp1ab-nsp7 pp1ab-nsp6 O-glycosyl 3atetramerpp1ab-nsp13 S-adenosyl-L-methionineGSK3B GTPST3GAL4 NTPm7G(5')pppAm-capped,polyadenylatedSARS-CoV-1subgenomic mRNAs(plus strand)pp1a nsp16:nsp10glycosylated-ACE2 pp1ab-nsp7 SUMO1-K62-ADPr-p-S177-Ncap m7GpppA-mRNA2 pp1a-nsp10m7G(5')pppAm-mRNA3 pp1ab-nsp3 MAP1LC3BZCRB1 pp1ab-nsp4 mRNA6 minus strand mRNA2 minus strand pp1abnsp3nsp8:MAP1LC3Bm7G(5')pppAm-capped,polyadenylated mRNA6 pp1a-nsp6 encapsidated SARScoronavirus genomicRNA (plus strand)SUMO1-K62-ADPr-p-S177-Ncap Ub-3xPalmC-E M pp1ab-nsp16 pp1a-nsp10 NAMM latticepp1a-nsp10 GANAB pp1ab-nsp10CTSL(292-333) pp1ab-nsp13 pp1ab-nsp7 pp1a-nsp3 pp1a-nsp6 H2Opp1ab-nsp13 complex N-glycan-PALM-Spike pp1a-nsp4 M ATPpp1a-nsp4 S-adenosyl-L-homocysteinepp1ab-nsp8 Ub-3xPalmC-E pp1ab-nsp4 UBC(1-76) ERalpha-glucosidasespp1ab-nsp3 nsp1ESCRT-IIIpp1ab-nsp15 Pitrimmed N-glycan-PALM-Spike m7GpppA-SARS-CoV-1plus strandsubgenomic mRNAspp1ab-nsp7 SUMO1-K62-ADPr-p-S177-Ncap nsp9pp1a-nsp7 Host Derived LipidBilayer MembranePPiH2O9bpp1a-nsp7 m7G(5')pppAm-capped,polyadenylated mRNA8 Cathepsin L1pp1ab-nsp7 mRNA5 Ub-3xPalmC-E pp1ab-nsp3 pp1a-nsp4 PRKCSH pp1a-nsp5 m7G(5')pppAm-capped,polyadenylated-mRNA9 N-glycan M m7GpppA-capped SARS-CoV-1 genomic RNA (plus strand) SUMO1-K62-p-S177-Ncap dimerpp1ab-nsp14 pp1ab-nsp8 N-glycan pp1a-nsp3 pp1a-nsp8 pp1a-nsp8pp1ab-nsp15 ADPr-p-S177-Ncapnucleotide-sugarUBC(77-152) UDP-N-acetyl-alpha-D-glucosamine(2−)CHMP6 m7G(5')pppAm-capped,polyadenylated mRNA7 pp1ab-nsp8 pp1ab-nsp14 m7G(5')pppAm-capped, polyadenylated SARS-CoV-1 genomic RNA (plus strand) ATP8bm7G(5')pppAm-capped, polyadenylated SARS-CoV-1 genomic RNA (plus strand) m7G(5')pppAm-capped,polyadenylated-mRNA9CTSL inhibitorspp1ab-nsp7 7a pp1a-nsp10 GALNT1RNA primer glycosylated-ACE2:ACE2 inhibitorspp1ab-nsp10 PiACE2DDX5 pp1a-nsp10 CTSL(114-288) mRNA9 minus strand pp1a-nsp6 M S-adenosyl-L-homocysteineN-glycan Spike3app1ab-nsp15 pp1ab-nsp15 pp1a-nsp3 pp1a-nsp7 N-glycan pp1ab-nsp3-4 pp1ab-nsp15 pp1ab-nsp12 SUMO1-K62-ADPr-p-S177-Ncap pp1a-nsp8 pp1ab-nsp14 pp1ab-nsp13 pp1a-nsp6 pp1ab-nsp3 CHMP4A pp1ab-nsp13 pp1ab-nsp4 VCPcomplex N-glycan-PALM-Spike S2 Fragment pp1a-nsp4 m7GpppA-capped SARS-CoV-1 genomic RNA (plus strand) H2OCHMP3 UBA52(1-76) pp1ab-nsp3-4 8b SARS-CoV-1 genomicRNA (plus strand)m7G(5')pppAm-mRNA6 nsp7pp1ab-nsp3 m7G(5')pppAm-cappedSARS-CoV-1 genomicRNA (plus strand)UBB(1-76) pp1ab-nsp4 H+nsp6pp1a-nsp3 pp1ab-nsp14 TMPRSS2:TMPRSS2inhibitorsSUMO1-K62-ADPr-p-S177-Ncap UBC(533-608) pp1ab-nsp8 m7G(5')pppAm-capped,polyadenylated mRNA2cepharanthine DDX5PIK3C3 pp1ab-nsp15 pp1ab-nsp6 SUMO1-K62-ADPr-p-S177-Ncap pp1a-nsp7 pp1ab-nsp12 pp1ab-nsp12 SUMO1-K62-ADPr-p-S177-Ncap pp1ab-nsp3 pp1a-nsp10 UBE2Ipp1ab-nsp8 pp1ab-nsp12 N-glycan M 7a pp1a-nsp7 H+N-glycan M pp1a-nsp3 pp1ab-nsp8 nsp7:nsp8:nsp12:nsp14:nsp10:nsp13O-glycosyl 3aSUMO1-K62-ADPr-p-S177-Ncap SUMO1-K62-ADPr-p-S177-Ncap N-glycan M S3:M:E:encapsidatedSARScoronavirusgenomicRNA:7a:O-glycosyl3atetramer:glycosylated-ACE2pp1a-nsp4 N-glycan nsp4S3:M:E:encapsidatedSARS coronavirusgenomic RNA:7a:O-glycosyl 3atetramerO-glycosyl 3a pp1a-nsp4 pp1a-nsp8 m7GpppA-capped SARS-CoV-1 genomic RNA (plus strand) Ub-3xPalmC-Epentamerpp1ab-nsp8 ADPSUMO1-K62-ADPr-p-S177-Ncap S-adenosyl-L-methioninepp1a-nsp7 mRNA4 minus strand pp1ab-nsp6 pp1ab-nsp10 GSKinsp6pp1ab-nsp4 SUMO-p-Ncap dimer3CLp dimerO-glycosyl 3a pp1a-nsp10 pp1a-nsp3 p-S177,S181,S185,S187,S189,S191,S195,T199,S203,S207-Npp1ab-nsp6 S3:M:E:encapsidatedSARS coronavirusgenomic RNA:7a:O-glycosyl 3atetramernascent Spikem7GpppA-capped SARS-CoV-1 genomic RNA (plus strand) pp1a-nsp4 pp1a-nsp7 m7G(5')pppAm-capped, polyadenylated SARS-CoV-1 genomic RNA (plus strand) m7GpppA-mRNA3 pp1a-nsp4 complex N-glycan-PALM-Spike trimmed N-glycan-PALM-Spike M pp1ab-nsp14 SARS-CoV-1 plusstrand subgenomicmRNAsUDP-GalNAcpp1ab-nsp3 pp1ab-nsp12GTPnucleoside5'-diphosphate(3-)NMPSUMO1-K62-ADPr-p-S177-Ncap pp1a-nsp8 N-glycan pp1ab-nsp3 MOGS pp1ab-nsp8 pp1ab-nsp4 SARS-CoV-1 gRNAcomplement (minusstrand):RTCpp1ab-nsp12 pp1a-nsp10 pp1a-nsp2 pp1a-nsp1-4UBC(609-684) pp1ab-nsp15 ATPpp1a-nsp6 SARS-CoV-1 genomicRNA complement(minus strand)PIK3R4 7a pp1ab-nsp12 pp1ab-nsp12 m7G(5')pppAm-capped,polyadenylated mRNA4SARS coronavirusgRNA with secondarystructure:RTCpp1a-nsp7 CHMP2A pp1ab-nsp15 mRNA8 NO-glycosyl 3a ATPH2Opp1a-nsp10 pp1ab-nsp1-4S3:M:E:encapsidatedSARS coronavirusgenomicRNA:O-glycosyl 3atetramerpp1ab-nsp9 Ub-3xPalmC-E CQ, HCQUBC(229-304) N-glycan pp1ab-nsp3 ADPO-glycosyl 3a Mlattice:Eprotein:encapsidated SARS coronavirus genomic RNApp1ab-nsp14 SUMO1-K62-ADPr-p-S177-Ncap pp1ab-nsp13 O-glycosyl 3a PARP10 SARScoronavirusgRNAwithsecondarystructure:RTC:nascent RNA minus strandnsp15 hexamerpp1ab-nsp10 SARS-CoV-1 nascent genomic RNA complement (minus strand) Ub-3xPalmC-E pp1a-nsp6 PPiN-glycan pp1a-nsp3-4 trimmed unfoldedN-glycan Spikenascent Enascent Mpp1a-nsp5 pp1a-nsp11PARP9 N-glycan M ST6GALNAC2 H+m7GpppA-mRNA8 N-glycan M N-glycan nsp3m7GpppA-cappedSARS-CoV-1 genomicRNA (plus strand)MAP1LC3B complex N-glycan-PALM-Spike PARP16 MAP1LC3Bpp1ab-nsp8 nsp10:nsp14pp1ab-nsp13O-glycosyl 3aUBE2I-G97-SUMO1 RTCpp1a-nsp6 pp1ab-nsp7 UBB(77-152) PPipp1ab-nsp13 pp1ab-nsp15S1:S2:M:E:7a:O-glycosyl 3atetramerpp1a-nsp1-4pp1a-nsp4 pp1ab-nsp8 ZCRB1PPinucleoside5'-diphosphate(3−)SARS coronavirusgRNA:RTC:RNA primerpp1ab-nsp7 m7G(5')pppAm-capped, polyadenylated SARS-CoV-1 genomic RNA (plus strand) TMPRSS2 mRNA9 CoA-SHpp1a-nsp8 m7G(5')pppAm-mRNA9 pp1ab-nsp16 NcaptrimmedN-glycan-PALM-Spikem7G(5')pppAm-mRNA4 nsp7:nsp8:nsp12:nsp14:nsp10pp1ab-nsp10 GTPpp1ab-nsp4 H2Opp1ab-nsp3 N-glycan M pp1a-nsp8 pp1ab-nsp16 m7GpppA-mRNA7 SUMO1-K62-ADPr-p-S177-Ncap pp1a-nsp4 SARS-CoV-1 genomic RNA (plus strand) m7G(5')pppAm-capped,polyadenylated mRNA2 nsp3:nsp4pp1ab-nsp16 SARS-CoV-1 gRNA:RTCm7G(5')pppAm-mRNA8 pp1ab-nsp3 CANXpp1ab-nsp6 pp1a-nsp8 pp1ab-nsp4 pp1ab-nsp16 H2Opp1a-nsp8 pp1a-nsp6-11ADP7aα-Ketoamidespp1ab-nsp12 GSK3VHLpp1ab-nsp15 H2OUBC(457-532) m7G(5')pppAm-capped,polyadenylated mRNA5 NTPm7G(5')pppAm-capped, polyadenylated SARS-CoV-1 genomic RNA (plus strand) N-glycan MM SARS-CoV-1gRNA:RTC:nascentRNA minus strandATPpp1a-nsp8 m7G(5')pppAm-capped, polyadenylated SARS-CoV-1 genomic RNA (plus strand) PPipp1a-nsp3 PPiMAP1LC3B pp1ab-nsp10 m7G(5')pppAm-capped, polyadenylated SARS-CoV-1 genomic RNA (plus strand) RTC inhibitorsO-glycosyl 3a pp1a-nsp5UVRAG complexRNA primer 94, 160, 162, 163, 177...94, 160, 162, 163, 177...94, 160, 162, 163, 177...94, 160, 162, 163, 177...11594, 160, 162, 163, 177...11511515394, 160, 162, 163, 177...11587, 89, 112, 114, 131...1151414115333115147594, 160, 162, 163, 177...94, 160, 162, 163, 177...159145394, 160, 162, 163, 177...16394, 160, 162, 163, 177...94, 160, 162, 163, 177...113106115741410611593141133310692, 1631494, 160, 162, 163, 177...757414394, 160, 162, 163, 177...37511210614115372115141494, 160, 162, 163, 177...141512211594, 160, 162, 163, 177...3331494, 160, 162, 163, 177...1494, 160, 162, 163, 177...3315394, 160, 162, 163, 177...11511533


Description

The SARS-CoV-1 coronavirus is the causative agent of the outbreak of severe acute respiratory syndrome in 2003 that caused 8,098 known cases of the disease and 774 deaths. The molecular events involved in viral infection and the response of the human host to it have since been studied in detail and are annotated here (de Wit et al. 2016; Marra et al. 2003). The SARS-CoV-1 viral infection pathway here uses entries listed in the UniProt "Human SARS coronavirus (SARS-CoV) (Severe acute respiratory syndrome coronavirus)" taxonomy.

SARS-CoV-1 infection begins with the binding of viral S (spike) protein to cell surface angiotensin converting enzyme 2 (ACE2) and endocytosis of the bound virion. Within the endocytic vesicle, host proteases mediate cleavage of S protein into S1 and S2 fragments, leading to S2-mediated fusion of the viral and host endosome membranes and release of the viral capsid into the host cell cytosol. The capsid is uncoated to free the viral genomic RNA, whose cap-dependent translation produces polyprotein pp1a and, by means of a 1-base frameshift, polyprotein pp1ab. Autoproteolytic cleavage of pp1a and pp1ab generates 15 or 16 nonstructural proteins (nsps) with various functions. Importantly, the RNA dependent RNA polymerase (RdRP) activity is encoded in nsp12. Nsp3, 4, and 6 induce rearrangement of the cellular endoplasmic reticulum membrane to form cytosolic double membrane vesicles (DMVs) where the viral replication transcription complex is assembled and anchored. With viral genomic RNA as a template, viral replicase-transcriptase synthesizes a full length negative sense antigenome, which in turn serves as a template for the synthesis of new genomic RNA. The replicase-transcriptase can also switch template during discontinuous transcription of the genome at transcription regulated sequences to produce a nested set of negative-sense subgenomic (sg) RNAs, which are used as templates for the synthesis of positive-sense sgRNAs that are translated to generate viral proteins. Finally, viral particle assembly occurs in the ER Golgi intermediate compartment (ERGIC). Viral M protein provides the scaffold for virion morphogenesis (Fung & Liu 2019; Masters 2006). View original pathway at Reactome.

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Reactome-Converter 
Pathway is converted from Reactome ID: 9678108
Reactome-version 
Reactome version: 75
Reactome Author 
Reactome Author: Gillespie, Marc E

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Bibliography

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  127. Tan YW, Hong W, Liu DX.; ''Binding of the 5'-untranslated region of coronavirus RNA to zinc finger CCHC-type and RNA-binding motif 1 enhances viral replication and transcription.''; PubMed Europe PMC Scholia
  128. Surjit M, Kumar R, Mishra RN, Reddy MK, Chow VT, Lal SK.; ''The severe acute respiratory syndrome coronavirus nucleocapsid protein is phosphorylated and localizes in the cytoplasm by 14-3-3-mediated translocation.''; PubMed Europe PMC Scholia
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  131. Bhardwaj K, Sun J, Holzenburg A, Guarino LA, Kao CC.; ''RNA recognition and cleavage by the SARS coronavirus endoribonuclease.''; PubMed Europe PMC Scholia
  132. Surjit M, Lal SK.; ''The SARS-CoV nucleocapsid protein: a protein with multifarious activities.''; PubMed Europe PMC Scholia
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  135. Fung TS, Liu DX.; ''Human Coronavirus: Host-Pathogen Interaction.''; PubMed Europe PMC Scholia
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  137. Li F, Li W, Farzan M, Harrison SC.; ''Structure of SARS coronavirus spike receptor-binding domain complexed with receptor.''; PubMed Europe PMC Scholia
  138. Cottam EM, Whelband MC, Wileman T.; ''Coronavirus NSP6 restricts autophagosome expansion.''; PubMed Europe PMC Scholia
  139. Voss D, Pfefferle S, Drosten C, Stevermann L, Traggiai E, Lanzavecchia A, Becker S.; ''Studies on membrane topology, N-glycosylation and functionality of SARS-CoV membrane protein.''; PubMed Europe PMC Scholia
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  141. Chen IY, Moriyama M, Chang MF, Ichinohe T.; ''Severe Acute Respiratory Syndrome Coronavirus Viroporin 3a Activates the NLRP3 Inflammasome.''; PubMed Europe PMC Scholia
  142. Chen S, Jonas F, Shen C, Hilgenfeld R.; ''Liberation of SARS-CoV main protease from the viral polyprotein: N-terminal autocleavage does not depend on the mature dimerization mode.''; PubMed Europe PMC Scholia
  143. McBride CE, Machamer CE.; ''A single tyrosine in the severe acute respiratory syndrome coronavirus membrane protein cytoplasmic tail is important for efficient interaction with spike protein.''; PubMed Europe PMC Scholia
  144. Ujike M, Huang C, Shirato K, Matsuyama S, Makino S, Taguchi F.; ''Two palmitylated cysteine residues of the severe acute respiratory syndrome coronavirus spike (S) protein are critical for S incorporation into virus-like particles, but not for M-S co-localization.''; PubMed Europe PMC Scholia
  145. Chen JY, Chen WN, Poon KM, Zheng BJ, Lin X, Wang YX, Wen YM.; ''Interaction between SARS-CoV helicase and a multifunctional cellular protein (Ddx5) revealed by yeast and mammalian cell two-hybrid systems.''; PubMed Europe PMC Scholia
  146. Bernini A, Spiga O, Venditti V, Prischi F, Bracci L, Huang J, Tanner JA, Niccolai N.; ''Tertiary structure prediction of SARS coronavirus helicase.''; PubMed Europe PMC Scholia
  147. Huang C, Ito N, Tseng CT, Makino S.; ''Severe acute respiratory syndrome coronavirus 7a accessory protein is a viral structural protein.''; PubMed Europe PMC Scholia
  148. Liao Y, Lescar J, Tam JP, Liu DX.; ''Expression of SARS-coronavirus envelope protein in Escherichia coli cells alters membrane permeability.''; PubMed Europe PMC Scholia
  149. Simmons G, Reeves JD, Rennekamp AJ, Amberg SM, Piefer AJ, Bates P.; ''Characterization of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) spike glycoprotein-mediated viral entry.''; PubMed Europe PMC Scholia
  150. Chang CK, Sue SC, Yu TH, Hsieh CM, Tsai CK, Chiang YC, Lee SJ, Hsiao HH, Wu WJ, Chang WL, Lin CH, Huang TH.; ''Modular organization of SARS coronavirus nucleocapsid protein.''; PubMed Europe PMC Scholia
  151. Song HC, Seo MY, Stadler K, Yoo BJ, Choo QL, Coates SR, Uematsu Y, Harada T, Greer CE, Polo JM, Pileri P, Eickmann M, Rappuoli R, Abrignani S, Houghton M, Han JH.; ''Synthesis and characterization of a native, oligomeric form of recombinant severe acute respiratory syndrome coronavirus spike glycoprotein.''; PubMed Europe PMC Scholia
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  153. Wu CH, Yeh SH, Tsay YG, Shieh YH, Kao CL, Chen YS, Wang SH, Kuo TJ, Chen DS, Chen PJ.; ''Glycogen synthase kinase-3 regulates the phosphorylation of severe acute respiratory syndrome coronavirus nucleocapsid protein and viral replication.''; PubMed Europe PMC Scholia
  154. Nieto-Torres JL, Dediego ML, Alvarez E, Jiménez-Guardeño JM, Regla-Nava JA, Llorente M, Kremer L, Shuo S, Enjuanes L.; ''Subcellular location and topology of severe acute respiratory syndrome coronavirus envelope protein.''; PubMed Europe PMC Scholia
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  156. Tanner JA, Watt RM, Chai YB, Lu LY, Lin MC, Peiris JS, Poon LL, Kung HF, Huang JD.; ''The severe acute respiratory syndrome (SARS) coronavirus NTPase/helicase belongs to a distinct class of 5' to 3' viral helicases.''; PubMed Europe PMC Scholia
  157. Tohge T, Nishiyama Y, Hirai MY, Yano M, Nakajima J, Awazuhara M, Inoue E, Takahashi H, Goodenowe DB, Kitayama M, Noji M, Yamazaki M, Saito K.; ''Functional genomics by integrated analysis of metabolome and transcriptome of Arabidopsis plants over-expressing an MYB transcription factor.''; PubMed Europe PMC Scholia
  158. Kumar S, Dare L, Vasko-Moser JA, James IE, Blake SM, Rickard DJ, Hwang SM, Tomaszek T, Yamashita DS, Marquis RW, Oh H, Jeong JU, Veber DF, Gowen M, Lark MW, Stroup G.; ''A highly potent inhibitor of cathepsin K (relacatib) reduces biomarkers of bone resorption both in vitro and in an acute model of elevated bone turnover in vivo in monkeys.''; PubMed Europe PMC Scholia
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History

View all...
CompareRevisionActionTimeUserComment
124662view13:42, 18 November 2022JfigueirahasbunUpdated viral protein shapes, identifiers and color
114721view16:20, 25 January 2021ReactomeTeamReactome version 75
113561view13:17, 2 November 2020DeSlOntology Term : 'viral infectious disease' added !
113560view13:16, 2 November 2020DeSlOntology Term : 'severe acute respiratory syndrome' added !
113547view12:29, 2 November 2020DeSlOntology Term : 'disease pathway' added !
113546view12:28, 2 November 2020DeSlOntology Term : 'infectious disease pathway' added !
113545view12:26, 2 November 2020DeSlRemoved empty complex drawing at top left corner
113544view12:24, 2 November 2020DeSlChanged layout for several complexes (included at least one small DataNode at top left corner, stretching the whole complex visually).
113541view12:02, 2 November 2020ReactomeTeamNew pathway

External references

DataNodes

View all...
NameTypeDatabase referenceComment
1-deoxynojirimycin
3CLp dimer:α-KetoamidesComplexR-COV-9681588 (Reactome)
3CLp dimerComplexR-COV-9684343 (Reactome)
3a:membranous structureComplexR-COV-9685958 (Reactome)
3aProteinP59632 (Uniprot-TrEMBL)
3xPalmC-EProteinP59637 (Uniprot-TrEMBL)
7a ProteinP59635 (Uniprot-TrEMBL)
7aProteinP59635 (Uniprot-TrEMBL)
8b ProteinQ80H93 (Uniprot-TrEMBL)
8b:MAP1LC3BComplexR-HSA-9687111 (Reactome)
8bProteinQ80H93 (Uniprot-TrEMBL)
9bProteinP59636 (Uniprot-TrEMBL)
ACE2 inhibitorsComplexR-ALL-9695417 (Reactome)
ACE2ProteinQ9BYF1 (Uniprot-TrEMBL)
ADPMetaboliteCHEBI:456216 (ChEBI)
ADPr-p-S177-NcapProteinP59595 (Uniprot-TrEMBL)
ATPMetaboliteCHEBI:30616 (ChEBI)
BECN1 ProteinQ14457 (Uniprot-TrEMBL)
CANXProteinP27824 (Uniprot-TrEMBL)
CHMP2A ProteinO43633 (Uniprot-TrEMBL)
CHMP2B ProteinQ9UQN3 (Uniprot-TrEMBL)
CHMP3 ProteinQ9Y3E7 (Uniprot-TrEMBL)
CHMP4A ProteinQ9BY43 (Uniprot-TrEMBL)
CHMP4B ProteinQ9H444 (Uniprot-TrEMBL)
CHMP4C ProteinQ96CF2 (Uniprot-TrEMBL)
CHMP6 ProteinQ96FZ7 (Uniprot-TrEMBL)
CHMP7 ProteinQ8WUX9 (Uniprot-TrEMBL)
CMP-Neu5AcMetaboliteCHEBI:16556 (ChEBI)
CMPMetaboliteCHEBI:17361 (ChEBI)
CQ, HCQComplexR-ALL-9685610 (Reactome)
CQ, HCQComplexR-ALL-9685614 (Reactome)
CQ2+
CQ2+, HCQ2+ComplexR-ALL-9685618 (Reactome)
CTSL inhibitorsComplexR-ALL-9693170 (Reactome)
CTSL(114-288) ProteinP07711 (Uniprot-TrEMBL)
CTSL(292-333) ProteinP07711 (Uniprot-TrEMBL)
CTSL:CTSL inhibitorsComplexR-HSA-9683316 (Reactome)
Cathepsin L1ComplexR-HSA-9686717 (Reactome)
CoA-SHMetaboliteCHEBI:15346 (ChEBI)
DDX5 ProteinP17844 (Uniprot-TrEMBL)
DDX5ProteinP17844 (Uniprot-TrEMBL)
ER alpha-glucosidasesComplexR-HSA-9682983 (Reactome)
ER-alpha glucosidases:ER-alpha glucosidase inhibitorsComplexR-HSA-9686842 (Reactome)
ER-alpha-glucosidase inhibitorsComplexR-ALL-9686811 (Reactome)
ESCRT-IIIComplexR-HSA-917723 (Reactome)
GALNT1ProteinQ10472 (Uniprot-TrEMBL)
GANAB ProteinQ14697 (Uniprot-TrEMBL)
GSK3A ProteinP49840 (Uniprot-TrEMBL)
GSK3B ProteinP49841 (Uniprot-TrEMBL)
GSK3B:GSKiComplexR-HSA-9687663 (Reactome)
GSK3BProteinP49841 (Uniprot-TrEMBL)
GSK3ComplexR-HSA-198358 (Reactome)
GSKiComplexR-ALL-9687688 (Reactome)
GTPMetaboliteCHEBI:15996 (ChEBI)
GalNAc-O-3aProteinP59632 (Uniprot-TrEMBL)
H+MetaboliteCHEBI:15378 (ChEBI)
H2OMetaboliteCHEBI:15377 (ChEBI)
HCQ
Host Derived Lipid Bilayer MembraneR-ALL-9685933 (Reactome)
Host Derived Lipid Bilayer Membrane R-ALL-9685947 (Reactome)
Li+
M

lattice:E

protein:encapsidated SARS coronavirus genomic RNA
ComplexR-COV-9684226 (Reactome)
M ProteinP0DTC5 (Uniprot-TrEMBL)
M ProteinP59596 (Uniprot-TrEMBL)
M latticeComplexR-COV-9684216 (Reactome)
MAP1LC3B ProteinQ9GZQ8 (Uniprot-TrEMBL)
MAP1LC3BProteinQ9GZQ8 (Uniprot-TrEMBL)
MGAT1ProteinP26572 (Uniprot-TrEMBL)
MOGS ProteinQ13724 (Uniprot-TrEMBL)
MProteinP0DTC5 (Uniprot-TrEMBL)
N-glycan pp1ab-nsp3-4ProteinP0C6X7 (Uniprot-TrEMBL)
N-glycan EProteinP59637 (Uniprot-TrEMBL)
N-glycan M ProteinP59596 (Uniprot-TrEMBL)
N-glycan MProteinP59596 (Uniprot-TrEMBL)
N-glycan SpikeProteinP59594 (Uniprot-TrEMBL)
N-glycan nsp3-4ComplexR-COV-9684863 (Reactome)
N-glycan nsp3ComplexR-COV-9682205 (Reactome)
N-glycan nsp4ComplexR-COV-9684875 (Reactome)
N-glycan pp1a-nsp3 ProteinP0C6U8 (Uniprot-TrEMBL)
N-glycan pp1a-nsp3-4 ProteinP0C6U8 (Uniprot-TrEMBL)
N-glycan pp1a-nsp4 ProteinP0C6U8 (Uniprot-TrEMBL)
N-glycan pp1ab-nsp3 ProteinP0C6X7 (Uniprot-TrEMBL)
N-glycan pp1ab-nsp3-4 ProteinP0C6X7 (Uniprot-TrEMBL)
N-glycan pp1ab-nsp4 ProteinP0C6X7 (Uniprot-TrEMBL)
NAD+MetaboliteCHEBI:57540 (ChEBI)
NAMMetaboliteCHEBI:17154 (ChEBI)
NHC
NMPMetaboliteCHEBI:26558 (ChEBI)
NProteinP0DTC9 (Uniprot-TrEMBL)
NTPMetaboliteCHEBI:17326 (ChEBI)
NcapProteinP59595 (Uniprot-TrEMBL)
O-glycosyl 3a tetramerComplexR-COV-9685937 (Reactome)
O-glycosyl 3a tetramerComplexR-COV-9685967 (Reactome)
O-glycosyl 3a tetramerComplexR-COV-9686674 (Reactome)
O-glycosyl 3a ProteinP59632 (Uniprot-TrEMBL)
O-glycosyl 3aProteinP59632 (Uniprot-TrEMBL)
PARP10 ProteinQ53GL7 (Uniprot-TrEMBL)
PARP14 ProteinQ460N5 (Uniprot-TrEMBL)
PARP16 ProteinQ8N5Y8 (Uniprot-TrEMBL)
PARP4 ProteinQ9UKK3 (Uniprot-TrEMBL)
PARP6 ProteinQ2NL67 (Uniprot-TrEMBL)
PARP8 ProteinQ8N3A8 (Uniprot-TrEMBL)
PARP9 ProteinQ8IXQ6 (Uniprot-TrEMBL)
PARPsComplexR-HSA-8938273 (Reactome)
PIK3C3 ProteinQ8NEB9 (Uniprot-TrEMBL)
PIK3R4 ProteinQ99570 (Uniprot-TrEMBL)
PPiMetaboliteCHEBI:29888 (ChEBI)
PRKCSH ProteinP14314 (Uniprot-TrEMBL)
PiMetaboliteCHEBI:43474 (ChEBI)
RB1 ProteinP06400 (Uniprot-TrEMBL)
RB1ProteinP06400 (Uniprot-TrEMBL)
RNA primer R-ALL-9681661 (Reactome)
RPS27A(1-76) ProteinP62979 (Uniprot-TrEMBL)
RTC inhibitorsComplexR-ALL-9687408 (Reactome)
RTCComplexR-COV-9686016 (Reactome)
S-adenosyl-L-homocysteineMetaboliteCHEBI:16680 (ChEBI)
S-adenosyl-L-methionineMetaboliteCHEBI:15414 (ChEBI)
S1:S2:M:E:

7a:O-glycosyl 3a

tetramer
ComplexR-COV-9686705 (Reactome)
S1:S2:M:E:encapsidated SARS coronavirus genomic RNA: 7a:O-glycosyl 3a tetramerComplexR-COV-9686703 (Reactome)
S3:M:E:encapsidated

SARS coronavirus genomic RNA: 7a:O-glycosyl 3a

tetramer:glycosylated-ACE2
ComplexR-HSA-9686311 (Reactome)
S3:M:E:encapsidated

SARS coronavirus genomic RNA: 7a:O-glycosyl 3a

tetramer:glycosylated-ACE2
ComplexR-HSA-9686692 (Reactome)
S3:M:E:encapsidated

SARS coronavirus genomic RNA:7a:O-glycosyl

3a tetramer
ComplexR-COV-9684225 (Reactome)
S3:M:E:encapsidated

SARS coronavirus genomic RNA:7a:O-glycosyl

3a tetramer
ComplexR-COV-9685539 (Reactome)
S3:M:E:encapsidated

SARS coronavirus genomic RNA:O-glycosyl 3a

tetramer
ComplexR-COV-9686310 (Reactome)
S3:M:E:encapsidated

SARS coronavirus genomic RNA: 7a:O-glycosyl 3a

tetramer
ComplexR-COV-9685506 (Reactome)
SARS

coronavirus gRNA with secondary

structure:RTC:nascent RNA minus strand
ComplexR-COV-9682692 (Reactome)
SARS coronavirus

gRNA with secondary

structure:RTC
ComplexR-COV-9682668 (Reactome)
SARS coronavirus

gRNA:RTC:RNA primer:RTC

inhibitors
ComplexR-COV-9680476 (Reactome)
SARS coronavirus gRNA:RTC:RNA primerComplexR-COV-9681663 (Reactome)
SARS coronavirus

gRNA:RTC:nascent RNA minus strand with mismatched

nucleotide
ComplexR-COV-9682566 (Reactome)
SARS coronavirus nascent genomic RNA complement (minus strand) with mismatched 3' nucleotide ProteinNC_004718.3 (NCBI Protein)
SARS-CoV-1

gRNA:RTC:nascent RNA minus strand:RTC

inhibitors
ComplexR-COV-9687385 (Reactome)
SARS-CoV-1

gRNA:RTC:nascent

RNA minus strand
ComplexR-COV-9682469 (Reactome)
SARS-CoV-1 gRNA

complement (minus strand):RTC:RTC

inhibitors
ComplexR-COV-9687382 (Reactome)
SARS-CoV-1 gRNA

complement (minus

strand):RTC
ComplexR-COV-9682253 (Reactome)
SARS-CoV-1 gRNA:RTCComplexR-COV-9681659 (Reactome)
SARS-CoV-1 genomic RNA (plus strand)RnaNC_004718.3 (NCBI Protein)
SARS-CoV-1 genomic

RNA complement

(minus strand)
RnaNC_004718.3 (NCBI Protein)
SARS-CoV-1 genomic RNA (plus strand) ProteinNC_004718.3 (NCBI Protein)
SARS-CoV-1 minus

strand subgenomic

mRNAs
ComplexR-COV-9685642 (Reactome)
SARS-CoV-1 nascent genomic RNA complement (minus strand) ProteinNC_004718.3 (NCBI Protein)
SARS-CoV-1 plus

strand subgenomic

mRNAs
ComplexR-COV-9685680 (Reactome)
ST3GAL1 ProteinQ11201 (Uniprot-TrEMBL)
ST3GAL2 ProteinQ16842 (Uniprot-TrEMBL)
ST3GAL3 ProteinQ11203 (Uniprot-TrEMBL)
ST3GAL4 ProteinQ11206 (Uniprot-TrEMBL)
ST6GAL1 ProteinP15907 (Uniprot-TrEMBL)
ST6GALNAC2 ProteinQ9UJ37 (Uniprot-TrEMBL)
ST6GALNAC3 ProteinQ8NDV1 (Uniprot-TrEMBL)
ST6GALNAC4 ProteinQ9H4F1 (Uniprot-TrEMBL)
SUMO-p-Ncap

dimer:SARS coronavirus genomic

RNA
ComplexR-COV-9684230 (Reactome)
SUMO-p-Ncap dimerComplexR-COV-9683761 (Reactome)
SUMO-p-Ncap dimerComplexR-COV-9686056 (Reactome)
SUMO1-C93-UBE2I ProteinP63279 (Uniprot-TrEMBL)
SUMO1-K62-ADPr-p-S177-Ncap ProteinP59595 (Uniprot-TrEMBL)
SUMO1-K62-ADPr-p-S177-NcapProteinP59595 (Uniprot-TrEMBL)
SUMO1-K62-p-S177-Ncap dimerComplexR-COV-9683649 (Reactome)
SUMO1-K62-p-S177-Ncap dimerComplexR-COV-9684203 (Reactome)
SUMO1:C93-UBE2IComplexR-HSA-4656922 (Reactome)
TMPRSS2 ProteinO15393 (Uniprot-TrEMBL)
TMPRSS2 inhibitorsComplexR-ALL-9682035 (Reactome)
TMPRSS2:TMPRSS2 inhibitorsComplexR-HSA-9681532 (Reactome)
TMPRSS2ProteinO15393 (Uniprot-TrEMBL)
UBA52(1-76) ProteinP62987 (Uniprot-TrEMBL)
UBB(1-76) ProteinP0CG47 (Uniprot-TrEMBL)
UBB(153-228) ProteinP0CG47 (Uniprot-TrEMBL)
UBB(77-152) ProteinP0CG47 (Uniprot-TrEMBL)
UBC(1-76) ProteinP0CG48 (Uniprot-TrEMBL)
UBC(153-228) ProteinP0CG48 (Uniprot-TrEMBL)
UBC(229-304) ProteinP0CG48 (Uniprot-TrEMBL)
UBC(305-380) ProteinP0CG48 (Uniprot-TrEMBL)
UBC(381-456) ProteinP0CG48 (Uniprot-TrEMBL)
UBC(457-532) ProteinP0CG48 (Uniprot-TrEMBL)
UBC(533-608) ProteinP0CG48 (Uniprot-TrEMBL)
UBC(609-684) ProteinP0CG48 (Uniprot-TrEMBL)
UBC(77-152) ProteinP0CG48 (Uniprot-TrEMBL)
UBE2I-G97-SUMO1 ProteinP63165 (Uniprot-TrEMBL)
UBE2IProteinP63279 (Uniprot-TrEMBL)
UDP-GalNAcMetaboliteCHEBI:16846 (ChEBI)
UDP-N-acetyl-alpha-D-glucosamine(2−)MetaboliteCHEBI:57705 (ChEBI)
UDPMetaboliteCHEBI:17659 (ChEBI)
UVRAG ProteinQ9P2Y5 (Uniprot-TrEMBL)
UVRAG complexComplexR-HSA-5683632 (Reactome) The PIK3C3-containing Beclin-1 complex consists of PIK3C3 (Vps34), BECN1 (Beclin-1, Atg6), PIK3R4 (p150, Vps15) and ATG14 (Barkor) (Matsunaga et al. 2009, Zhong et al. 2009). A similar complex where ATG14 is replaced by UVRAG functions later in autophagosome maturation and endocytic traffic (Itakura et al. 2008, Liang et al. 2008). Binding of KIAA0226 to this complex negatively regulates the maturation process (Matsunaga et al. 2009).
Ub-3xPalmC-E pentamerComplexR-COV-9683621 (Reactome)
Ub-3xPalmC-E pentamerComplexR-COV-9683623 (Reactome)
Ub-3xPalmC-E ProteinP59637 (Uniprot-TrEMBL)
Ub-3xPalmC-EProteinP59637 (Uniprot-TrEMBL)
UbComplexR-HSA-8943136 (Reactome)
VCPProteinP55072 (Uniprot-TrEMBL)
VHL ProteinP40337 (Uniprot-TrEMBL)
VHLProteinP40337 (Uniprot-TrEMBL)
ZCRB1 ProteinQ8TBF4 (Uniprot-TrEMBL)
ZCRB1:SARS-CoV-1

genomic RNA (plus

strand)
ComplexR-HSA-9682008 (Reactome)
ZCRB1ProteinQ8TBF4 (Uniprot-TrEMBL)
a nucleotide sugarMetaboliteCHEBI:25609 (ChEBI)
beta-D-glucoseMetaboliteCHEBI:15903 (ChEBI)
camostat
cepharanthine 10206 (PubChem-compound)
complex

N-glycan-PALM-Spike

trimer
ComplexR-COV-9683768 (Reactome)
complex N-glycan-PALM-Spike ProteinP59594 (Uniprot-TrEMBL)
complex N-glycan-PALM-Spike S1 Fragment ProteinP59594 (Uniprot-TrEMBL)
complex N-glycan-PALM-Spike S2 Fragment ProteinP59594 (Uniprot-TrEMBL)
compound 11r
encapsidated SARS

coronavirus genomic

RNA (plus strand)
ComplexR-COV-9686697 (Reactome)
encapsidated SARS

coronavirus genomic

RNA
ComplexR-COV-9684199 (Reactome)
glycosylated-ACE2 ProteinQ9BYF1 (Uniprot-TrEMBL)
glycosylated-ACE2:ACE2 inhibitorsComplexR-HSA-9695376 (Reactome)
glycosylated-ACE2ProteinQ9BYF1 (Uniprot-TrEMBL)
m7G(5')pppAm-SARS-CoV-1 plus strand subgenomic mRNAsComplexR-COV-9685891 (Reactome)
m7G(5')pppAm-capped

SARS-CoV-1 genomic

RNA (plus strand)
RnaNC_004718.3 (NCBI Protein)
m7G(5')pppAm-capped

SARS-CoV-1 genomic RNA complement

(minus strand)
RnaNC_004718.3 (NCBI Protein)
m7G(5')pppAm-capped SARS-CoV-1 genomic RNA complement (minus strand) ProteinNC_004718.3 (NCBI Protein)
m7G(5')pppAm-capped,

polyadenylated SARS-CoV-1 subgenomic mRNAs

(plus strand)
ComplexR-COV-9685910 (Reactome)
m7G(5')pppAm-capped,

polyadenylated SARS-CoV-1 genomic

RNA (plus strand)
RnaNC_004718.3 (NCBI Protein)
m7G(5')pppAm-capped, polyadenylated SARS-CoV-1 genomic RNA (plus strand) ProteinNC_004718.3 (NCBI Protein)
m7G(5')pppAm-capped,polyadenylated mRNA2 ProteinNC_004718.3 (NCBI Protein)
m7G(5')pppAm-capped,polyadenylated mRNA2RnaNC_004718.3 (NCBI Protein)
m7G(5')pppAm-capped,polyadenylated mRNA3 ProteinNC_004718.3 (NCBI Protein)
m7G(5')pppAm-capped,polyadenylated mRNA3RnaNC_004718.3 (NCBI Protein)
m7G(5')pppAm-capped,polyadenylated mRNA4 ProteinNC_004718.3 (NCBI Protein)
m7G(5')pppAm-capped,polyadenylated mRNA4RnaNC_004718.3 (NCBI Protein)
m7G(5')pppAm-capped,polyadenylated mRNA5 ProteinNC_004718.3 (NCBI Protein)
m7G(5')pppAm-capped,polyadenylated mRNA5RnaNC_004718.3 (NCBI Protein)
m7G(5')pppAm-capped,polyadenylated mRNA6 ProteinNC_004718.3 (NCBI Protein)
m7G(5')pppAm-capped,polyadenylated mRNA7 ProteinNC_004718.3 (NCBI Protein)
m7G(5')pppAm-capped,polyadenylated mRNA8 ProteinNC_004718.3 (NCBI Protein)
m7G(5')pppAm-capped,polyadenylated-mRNA9 ProteinNC_004718.3 (NCBI Protein)
m7G(5')pppAm-capped,polyadenylated-mRNA9RnaNC_004718.3 (NCBI Protein)
m7G(5')pppAm-mRNA2 ProteinNC_004718.3 (NCBI Protein)
m7G(5')pppAm-mRNA3 ProteinNC_004718.3 (NCBI Protein)
m7G(5')pppAm-mRNA4 ProteinNC_004718.3 (NCBI Protein)
m7G(5')pppAm-mRNA5 ProteinNC_004718.3 (NCBI Protein)
m7G(5')pppAm-mRNA6 ProteinNC_004718.3 (NCBI Protein)
m7G(5')pppAm-mRNA7 ProteinNC_004718.3 (NCBI Protein)
m7G(5')pppAm-mRNA8 ProteinNC_004718.3 (NCBI Protein)
m7G(5')pppAm-mRNA9 ProteinNC_004718.3 (NCBI Protein)
m7GpppA-SARS-CoV-1

plus strand

subgenomic mRNAs
ComplexR-COV-9685874 (Reactome)
m7GpppA-capped

SARS-CoV-1 genomic

RNA (plus strand)
RnaNC_004718.3 (NCBI Protein)
m7GpppA-capped

SARS-CoV-1 genomic RNA complement

(minus strand)
RnaNC_004718.3 (NCBI Protein)
m7GpppA-capped SARS-CoV-1 genomic RNA (plus strand) ProteinNC_004718.3 (NCBI Protein)
m7GpppA-mRNA2 ProteinNC_004718.3 (NCBI Protein)
m7GpppA-mRNA3 ProteinNC_004718.3 (NCBI Protein)
m7GpppA-mRNA4 ProteinNC_004718.3 (NCBI Protein)
m7GpppA-mRNA5 ProteinNC_004718.3 (NCBI Protein)
m7GpppA-mRNA6 ProteinNC_004718.3 (NCBI Protein)
m7GpppA-mRNA7 ProteinNC_004718.3 (NCBI Protein)
m7GpppA-mRNA8 ProteinNC_004718.3 (NCBI Protein)
m7GpppA-mRNA9 ProteinNC_004718.3 (NCBI Protein)
mRNA2 ProteinNC_004718.3 (NCBI Protein)
mRNA2 minus strand ProteinNC_004718.3 (NCBI Protein)
mRNA3 ProteinNC_004718.3 (NCBI Protein)
mRNA3 minus strand ProteinNC_004718.3 (NCBI Protein)
mRNA4 ProteinNC_004718.3 (NCBI Protein)
mRNA4 minus strand ProteinNC_004718.3 (NCBI Protein)
mRNA5 ProteinNC_004718.3 (NCBI Protein)
mRNA5 minus strand ProteinNC_004718.3 (NCBI Protein)
mRNA6 ProteinNC_004718.3 (NCBI Protein)
mRNA6 minus strand ProteinNC_004718.3 (NCBI Protein)
mRNA7 ProteinNC_004718.3 (NCBI Protein)
mRNA7 minus strand ProteinNC_004718.3 (NCBI Protein)
mRNA8 ProteinNC_004718.3 (NCBI Protein)
mRNA8 minus strand ProteinNC_004718.3 (NCBI Protein)
mRNA9 ProteinNC_004718.3 (NCBI Protein)
mRNA9 minus strand ProteinNC_004718.3 (NCBI Protein)
mefloquine
nascent EProteinP59637 (Uniprot-TrEMBL)
nascent MProteinP59596 (Uniprot-TrEMBL)
nascent SpikeProteinP59594 (Uniprot-TrEMBL)
nsp1-4ComplexR-COV-9684866 (Reactome)
nsp10:nsp14ComplexR-COV-9682545 (Reactome)
nsp10ProteinPRO_0000449628 (Uniprot-TrEMBL)
nsp13:DDX5ComplexR-HSA-9682634 (Reactome)
nsp15 hexamerComplexR-COV-9682715 (Reactome)
nsp15:RB1ComplexR-HSA-9682726 (Reactome)
nsp16:VHLComplexR-HSA-9683453 (Reactome)
nsp16:nsp10ComplexR-COV-9683433 (Reactome)
nsp1ComplexPRO_0000449619 (Uniprot-TrEMBL)
nsp2ProteinPRO_0000449620 (Uniprot-TrEMBL)
nsp3-4ComplexR-COV-9684869 (Reactome)
nsp3:nsp4:nsp6ComplexR-COV-9686008 (Reactome)
nsp3:nsp4ComplexR-COV-9686003 (Reactome)
nsp3ProteinPRO_0000449621 (Uniprot-TrEMBL)
nsp4ProteinPRO_0000449622 (Uniprot-TrEMBL)
nsp5ProteinPRO_0000449623 (Uniprot-TrEMBL)
nsp6ProteinPRO_0000449624 (Uniprot-TrEMBL)
nsp7:nsp8:nsp12:nsp14:nsp10:nsp13:nsp15ComplexR-COV-9683403 (Reactome)
nsp7:nsp8:nsp12:nsp14:nsp10:nsp13ComplexR-COV-9682616 (Reactome)
nsp7:nsp8:nsp12:nsp14:nsp10ComplexR-COV-9682451 (Reactome)
nsp7:nsp8:nsp12ComplexR-COV-9680807 (Reactome)
nsp7:nsp8ComplexR-COV-9680806 (Reactome)
nsp7ProteinPRO_0000449625 (Uniprot-TrEMBL)
nsp8:MAP1LC3BComplexR-HSA-9687117 (Reactome)
nsp8ComplexPRO_0000449626 (Uniprot-TrEMBL)
nsp9 dimerComplexR-COV-9684862 (Reactome)
nsp9ProteinPRO_0000449627 (Uniprot-TrEMBL)
nucleoside 5'-diphosphate(3-)MetaboliteCHEBI:57930 (ChEBI)
nucleoside 5'-diphosphate(3−)R-ALL-9683046 (Reactome)
nucleotide-sugarR-ALL-9683033 (Reactome)
p-S177,S181,S185,S187,S189,S191,S195,T199,S203,S207-NProteinP59595 (Uniprot-TrEMBL)
p-S177-NcapProteinP59595 (Uniprot-TrEMBL)
palmitoyl-CoAMetaboliteCHEBI:15525 (ChEBI)
pp1a ProteinP0C6U8 (Uniprot-TrEMBL)
pp1a dimerComplexR-COV-9684326 (Reactome)
pp1a-nsp1 ProteinP0C6U8 (Uniprot-TrEMBL)
pp1a-nsp1-4 ProteinP0C6U8 (Uniprot-TrEMBL)
pp1a-nsp1-4ProteinP0C6U8 (Uniprot-TrEMBL)
pp1a-nsp10 ProteinP0C6U8 (Uniprot-TrEMBL)
pp1a-nsp10ProteinP0C6U8 (Uniprot-TrEMBL)
pp1a-nsp11ProteinP0C6U8 (Uniprot-TrEMBL)
pp1a-nsp2 ProteinP0C6U8 (Uniprot-TrEMBL)
pp1a-nsp3 ProteinP0C6U8 (Uniprot-TrEMBL)
pp1a-nsp3-4 ProteinP0C6U8 (Uniprot-TrEMBL)
pp1a-nsp4 ProteinP0C6U8 (Uniprot-TrEMBL)
pp1a-nsp5 ProteinP0C6U8 (Uniprot-TrEMBL)
pp1a-nsp5ProteinP0C6U8 (Uniprot-TrEMBL)
pp1a-nsp6 ProteinP0C6U8 (Uniprot-TrEMBL)
pp1a-nsp6-11ProteinP0C6U8 (Uniprot-TrEMBL)
pp1a-nsp6ProteinP0C6U8 (Uniprot-TrEMBL)
pp1a-nsp7 ProteinP0C6U8 (Uniprot-TrEMBL)
pp1a-nsp7ProteinP0C6U8 (Uniprot-TrEMBL)
pp1a-nsp8 ProteinP0C6U8 (Uniprot-TrEMBL)
pp1a-nsp8ProteinP0C6U8 (Uniprot-TrEMBL)
pp1a-nsp9 ProteinP0C6U8 (Uniprot-TrEMBL)
pp1a-nsp9ProteinP0C6U8 (Uniprot-TrEMBL)
pp1aProteinP0C6U8 (Uniprot-TrEMBL)
pp1ab-nsp1 ProteinP0C6X7 (Uniprot-TrEMBL)
pp1ab-nsp1-4 ProteinP0C6X7 (Uniprot-TrEMBL)
pp1ab-nsp1-4ProteinP0C6X7 (Uniprot-TrEMBL)
pp1ab-nsp10 ProteinP0C6X7 (Uniprot-TrEMBL)
pp1ab-nsp10ProteinP0C6X7 (Uniprot-TrEMBL)
pp1ab-nsp12 ProteinP0C6X7 (Uniprot-TrEMBL)
pp1ab-nsp12ProteinP0C6X7 (Uniprot-TrEMBL)
pp1ab-nsp13 ProteinP0C6X7 (Uniprot-TrEMBL)
pp1ab-nsp13ProteinP0C6X7 (Uniprot-TrEMBL)
pp1ab-nsp14 ProteinP0C6X7 (Uniprot-TrEMBL)
pp1ab-nsp14ProteinP0C6X7 (Uniprot-TrEMBL)
pp1ab-nsp15 ProteinP0C6X7 (Uniprot-TrEMBL)
pp1ab-nsp15ProteinP0C6X7 (Uniprot-TrEMBL)
pp1ab-nsp16 ProteinP0C6X7 (Uniprot-TrEMBL)
pp1ab-nsp16ProteinP0C6X7 (Uniprot-TrEMBL)
pp1ab-nsp2 ProteinP0C6X7 (Uniprot-TrEMBL)
pp1ab-nsp3 ProteinP0C6X7 (Uniprot-TrEMBL)
pp1ab-nsp3-4 ProteinP0C6X7 (Uniprot-TrEMBL)
pp1ab-nsp4 ProteinP0C6X7 (Uniprot-TrEMBL)
pp1ab-nsp5 ProteinP0C6X7 (Uniprot-TrEMBL)
pp1ab-nsp5ProteinP0C6X7 (Uniprot-TrEMBL)
pp1ab-nsp6 ProteinP0C6X7 (Uniprot-TrEMBL)
pp1ab-nsp6ProteinP0C6X7 (Uniprot-TrEMBL)
pp1ab-nsp7 ProteinP0C6X7 (Uniprot-TrEMBL)
pp1ab-nsp7ProteinP0C6X7 (Uniprot-TrEMBL)
pp1ab-nsp8 ProteinP0C6X7 (Uniprot-TrEMBL)
pp1ab-nsp8ProteinP0C6X7 (Uniprot-TrEMBL)
pp1ab-nsp9 ProteinP0C6X7 (Uniprot-TrEMBL)
pp1ab-nsp9ProteinP0C6X7 (Uniprot-TrEMBL)
pp1abProteinP0C6X7 (Uniprot-TrEMBL)
sialyltransferasesComplexR-HSA-9683042 (Reactome)
teicoplanin
trimmed

N-glycan-PALM-Spike

trimer
ComplexR-COV-9683675 (Reactome)
trimmed

N-glycan-PALM-Spike

trimer
ComplexR-COV-9683676 (Reactome)
trimmed N-glycan-PALM-SpikeProteinP59594 (Uniprot-TrEMBL)
trimmed N-glycan SpikeProteinP59594 (Uniprot-TrEMBL)
trimmed N-glycan-PALM-Spike ProteinP59594 (Uniprot-TrEMBL)
trimmed unfolded N-glycan SpikeProteinP59594 (Uniprot-TrEMBL)
α-KetoamidesComplexR-ALL-9682022 (Reactome)

Annotated Interactions

View all...
SourceTargetTypeDatabase referenceComment
3CLp dimer:α-KetoamidesArrowR-HSA-9681596 (Reactome)
3CLp dimer:α-KetoamidesTBarR-HSA-9684273 (Reactome)
3CLp dimer:α-KetoamidesTBarR-HSA-9684309 (Reactome)
3CLp dimer:α-KetoamidesTBarR-HSA-9684340 (Reactome)
3CLp dimerArrowR-HSA-9684323 (Reactome)
3CLp dimerR-HSA-9681596 (Reactome)
3CLp dimermim-catalysisR-HSA-9684273 (Reactome)
3CLp dimermim-catalysisR-HSA-9684309 (Reactome)
3CLp dimermim-catalysisR-HSA-9684340 (Reactome)
3a:membranous structureArrowR-HSA-9685956 (Reactome)
3aArrowR-HSA-9683618 (Reactome)
3aArrowR-HSA-9683712 (Reactome)
3aR-HSA-9683712 (Reactome)
3aR-HSA-9683760 (Reactome)
3xPalmC-EArrowR-HSA-9683720 (Reactome)
3xPalmC-ER-HSA-9683679 (Reactome)
7aR-HSA-9686174 (Reactome)
8b:MAP1LC3BArrowR-HSA-9687109 (Reactome)
8bArrowR-HSA-9687435 (Reactome)
8bR-HSA-9687109 (Reactome)
9bArrowR-HSA-9687435 (Reactome)
ACE2 inhibitorsR-HSA-9695415 (Reactome)
ACE2ArrowR-HSA-9686731 (Reactome)
ADPArrowR-HSA-9681627 (Reactome)
ADPArrowR-HSA-9682695 (Reactome)
ADPArrowR-HSA-9683664 (Reactome)
ADPr-p-S177-NcapArrowR-HSA-9686061 (Reactome)
ADPr-p-S177-NcapR-HSA-9683687 (Reactome)
ATPR-HSA-9681627 (Reactome)
ATPR-HSA-9682695 (Reactome)
ATPR-HSA-9683664 (Reactome)
ATPR-HSA-9685519 (Reactome)
ATPR-HSA-9685906 (Reactome)
ArrowR-HSA-9687435 (Reactome)
CANXmim-catalysisR-HSA-9683772 (Reactome)
CMP-Neu5AcR-HSA-9683769 (Reactome)
CMPArrowR-HSA-9683769 (Reactome)
CQ, HCQArrowR-HSA-9683478 (Reactome)
CQ, HCQR-HSA-9683467 (Reactome)
CQ, HCQR-HSA-9683478 (Reactome)
CQ2+, HCQ2+ArrowR-HSA-9683467 (Reactome)
CTSL inhibitorsR-HSA-9685655 (Reactome)
CTSL:CTSL inhibitorsArrowR-HSA-9685655 (Reactome)
CTSL:CTSL inhibitorsTBarR-HSA-9686710 (Reactome)
Cathepsin L1R-HSA-9685655 (Reactome)
Cathepsin L1mim-catalysisR-HSA-9686710 (Reactome)
CoA-SHArrowR-HSA-9683653 (Reactome)
CoA-SHArrowR-HSA-9683720 (Reactome)
DDX5R-HSA-9682631 (Reactome)
ER alpha-glucosidasesR-HSA-9686790 (Reactome)
ER alpha-glucosidasesmim-catalysisR-HSA-9683663 (Reactome)
ER-alpha glucosidases:ER-alpha glucosidase inhibitorsArrowR-HSA-9686790 (Reactome)
ER-alpha glucosidases:ER-alpha glucosidase inhibitorsTBarR-HSA-9683663 (Reactome)
ER-alpha-glucosidase inhibitorsR-HSA-9686790 (Reactome)
ESCRT-IIIArrowR-HSA-9687435 (Reactome)
GALNT1mim-catalysisR-HSA-9683760 (Reactome)
GSK3B:GSKiArrowR-HSA-9687724 (Reactome)
GSK3B:GSKiTBarR-HSA-9683664 (Reactome)
GSK3BR-HSA-9687724 (Reactome)
GSK3Bmim-catalysisR-HSA-9683664 (Reactome)
GSK3mim-catalysisR-HSA-9681627 (Reactome)
GSKiR-HSA-9687724 (Reactome)
GTPR-HSA-9684016 (Reactome)
GTPR-HSA-9684017 (Reactome)
GTPR-HSA-9684018 (Reactome)
GalNAc-O-3aArrowR-HSA-9683760 (Reactome)
GalNAc-O-3aR-HSA-9683769 (Reactome)
H+ArrowR-HSA-9683648 (Reactome)
H+ArrowR-HSA-9683664 (Reactome)
H+ArrowR-HSA-9683669 (Reactome)
H+ArrowR-HSA-9683751 (Reactome)
H+ArrowR-HSA-9683755 (Reactome)
H+ArrowR-HSA-9683760 (Reactome)
H+ArrowR-HSA-9684261 (Reactome)
H+ArrowR-HSA-9684275 (Reactome)
H+ArrowR-HSA-9684290 (Reactome)
H+ArrowR-HSA-9686061 (Reactome)
H+R-HSA-9683467 (Reactome)
H2OR-HSA-9682603 (Reactome)
H2OR-HSA-9683663 (Reactome)
H2OR-HSA-9684016 (Reactome)
H2OR-HSA-9684017 (Reactome)
H2OR-HSA-9684018 (Reactome)
H2OR-HSA-9684273 (Reactome)
H2OR-HSA-9684309 (Reactome)
H2OR-HSA-9684321 (Reactome)
H2OR-HSA-9684336 (Reactome)
H2OR-HSA-9684340 (Reactome)
H2OR-HSA-9684351 (Reactome)
H2OR-HSA-9684352 (Reactome)
Host Derived Lipid Bilayer MembraneR-HSA-9685956 (Reactome)
M

lattice:E

protein:encapsidated SARS coronavirus genomic RNA
ArrowR-HSA-9684238 (Reactome)
M

lattice:E

protein:encapsidated SARS coronavirus genomic RNA
R-HSA-9684241 (Reactome)
M latticeArrowR-HSA-9684218 (Reactome)
M latticeR-HSA-9684238 (Reactome)
MAP1LC3BArrowR-HSA-9687435 (Reactome)
MAP1LC3BR-HSA-9687109 (Reactome)
MAP1LC3BR-HSA-9687121 (Reactome)
MAP1LC3BR-HSA-9687435 (Reactome)
MArrowR-HSA-9683718 (Reactome)
MGAT1mim-catalysisR-HSA-9683648 (Reactome)
MR-HSA-9684218 (Reactome)
N-glycan pp1ab-nsp3-4mim-catalysisR-HSA-9684352 (Reactome)
N-glycan EArrowR-HSA-9683669 (Reactome)
N-glycan MArrowR-HSA-9683734 (Reactome)
N-glycan MArrowR-HSA-9683751 (Reactome)
N-glycan MR-HSA-9683734 (Reactome)
N-glycan MR-HSA-9684218 (Reactome)
N-glycan SpikeArrowR-HSA-9683755 (Reactome)
N-glycan SpikeR-HSA-9683663 (Reactome)
N-glycan nsp3-4ArrowR-HSA-9684275 (Reactome)
N-glycan nsp3ArrowR-HSA-9684290 (Reactome)
N-glycan nsp3R-HSA-9686015 (Reactome)
N-glycan nsp3mim-catalysisR-HSA-9684321 (Reactome)
N-glycan nsp4ArrowR-HSA-9684261 (Reactome)
N-glycan nsp4R-HSA-9686015 (Reactome)
NAD+R-HSA-9686061 (Reactome)
NAMArrowR-HSA-9686061 (Reactome)
NArrowR-HSA-9685639 (Reactome)
NMPArrowR-HSA-9682603 (Reactome)
NR-HSA-9681627 (Reactome)
NTPR-HSA-9681651 (Reactome)
NTPR-HSA-9681674 (Reactome)
NTPR-HSA-9681840 (Reactome)
NTPR-HSA-9682465 (Reactome)
NTPR-HSA-9682563 (Reactome)
NTPR-HSA-9685639 (Reactome)
NTPR-HSA-9685681 (Reactome)
NcapArrowR-HSA-9683714 (Reactome)
NcapArrowR-HSA-9683735 (Reactome)
NcapR-HSA-9683664 (Reactome)
NcapR-HSA-9683714 (Reactome)
O-glycosyl 3a tetramerArrowR-HSA-9683746 (Reactome)
O-glycosyl 3a tetramerArrowR-HSA-9685950 (Reactome)
O-glycosyl 3a tetramerR-HSA-9685939 (Reactome)
O-glycosyl 3a tetramerR-HSA-9685950 (Reactome)
O-glycosyl 3a tetramerR-HSA-9685956 (Reactome)
O-glycosyl 3a tetramerR-HSA-9686174 (Reactome)
O-glycosyl 3aArrowR-HSA-9683769 (Reactome)
O-glycosyl 3aArrowR-HSA-9685939 (Reactome)
O-glycosyl 3aR-HSA-9683746 (Reactome)
PARPsmim-catalysisR-HSA-9686061 (Reactome)
PPiArrowR-HSA-9681651 (Reactome)
PPiArrowR-HSA-9681674 (Reactome)
PPiArrowR-HSA-9681840 (Reactome)
PPiArrowR-HSA-9682465 (Reactome)
PPiArrowR-HSA-9682563 (Reactome)
PPiArrowR-HSA-9684016 (Reactome)
PPiArrowR-HSA-9684017 (Reactome)
PPiArrowR-HSA-9684018 (Reactome)
PPiArrowR-HSA-9685519 (Reactome)
PPiArrowR-HSA-9685639 (Reactome)
PPiArrowR-HSA-9685681 (Reactome)
PPiArrowR-HSA-9685906 (Reactome)
PiArrowR-HSA-9682695 (Reactome)
PiArrowR-HSA-9684016 (Reactome)
PiArrowR-HSA-9684017 (Reactome)
PiArrowR-HSA-9684018 (Reactome)
R-HSA-9678128 (Reactome) SARS-CoV-1 spike (S3a) protein, as a component of the S3:M:E:encapsidated SARS coronavirus genomic RNA: 7a:O-glycosyl 3a tetramer complex, binds to glycosylated angiotensin converting enzyme 2 (ACE2) associated with the human host cell plasma membrane. Structural studies of the interaction between human ACE2 protein and the receptor-binding domain of S3a protein have identified key amino acid residues in both proteins responsible for their high-affinity interaction. These residues may be a key factor determining severity (and possibly human-to-human transmission) of SARS-CoV-1 (Li et al. 2003, 2005). The roles of S protein in viral binding to the host cell membrane and fusion of viral and host cell membranes and thus the central role of S protein in determining the host range and tissue tropisms of the virus are reviewed by Belouzard et al. (2012).
R-HSA-9680262 (Reactome) Remdesivir (GS-5734) is an investigational nucleotide analogue drug that was developed for its broad spectrum antiviral potential against Ebola and Marburg virus activity (Siegel et al. 2017). It targets and inhibitis viral RNA-dependent RNA polymerase (nsp12, RdRP), the key component of the replication transcription complex (RTC) (Agostini et al. 2018, Brown et al. 2019, Gordon et al. 2020). Remdesivir is being investigated for potential antiviral activity against SARS-CoV-2 by targeting viral replication (Agostini et al. 2018). Gordon et al. demonstrate remdesivir possesses broad antiviral activity against RNA viruses, including SARS-CoV, MERS-CoV and SARS-CoV-2 in-vitro (Gordon et al. 2020b). It could prevent asymptomatic, mild or moderate COVID-19 cases from progressing to severe disease (clinical trials NCT04252664, NCT04257656) but results so far in infected people have been mixed.

EIDD-2801, is an isopropylester prodrug of the ribonucleoside analogue N4-hydroxycytidine (NHC, EIDD-1931) that shows broad spectrum antiviral activity against various RNA viruses including Ebola, Influenza and CoV (Toots et al. 2019). NHC acts as a competitive alternative substrate for virally encoded RNA-dependent RNA polymerases. NHC was shown to inhibit multiple genetically-distinct Bat-CoV viruses in human primary epithelial cells without affecting cell viability. Prophylactic/therapeutic oral administration of NHC reduced lung titers and prevented acute lung failure in C57B/6 mice infected with CoV. The potency of NHC against multiple coronaviruses, its therapeutic efficacy, and oral bioavailability in vivo, all highlight its potential as an effective antiviral against SARS-CoV-2 and other future zoonotic coronaviruses (Sheahan et al. 2020).
R-HSA-9680811 (Reactome) The nsp7:nsp8 heterodimer binds to the RNA-directed RNA polymerase (nsp12) of the human SARS coronavirus on the polymerase thumb domain facing the NTP entry channel. Binding in this position sandwiches the RNA polymerase index finger loop between nsp7:nsp8 and the polymerase thumbdomain. The nsp7:nsp8 heterodimer may facilitate the interaction of the viral RNA polymerase with additional components of the RNA synthesis machinery. The second subunit of nsp8 interacts with the viral RNA polymerase interface domain proximal to the finger domain and the RNA template-binding channel, and is not bound to nsp7 (Kirchdoerfer and Ward 2019). This is consistent with the stoichiometry of the complex between feline coronavirus proteins nsp7, nsp8 and nsp12 (Xiao et al. 2012).
R-HSA-9680812 (Reactome) Human SARS coronavirus nonstructural proteins nsp7 and nsp8 form a heterodimer (Kirchdoerfer and Ward 2019). The nsp7:nsp8 complex may function as a hexadecamer, composed of 8 subunits of nsp7 and 8 subunits of nsp8 (Zhai et al. 2005).
R-HSA-9681314 (Reactome) The replication transcription complex (RTC) binds to the 3' end of the viral plus strand genomic RNA to initiate synthesis of the complementary minus strand. A 36 nucleotide sequence from the 3’-UTR of the plus strand, predicted to form a stable stem-loop structure, seems to be the minimal cis-acting RNA element required for the viral RNA-directed RNA polymerase (nsp12) to initiate RNA synthesis. The polyA tail also seems to play a role in the initiation of replication of viral genomic RNA (Ahn et al. 2012).
R-HSA-9681514 (Reactome) Entry of influenza, parainfluenza and coronaviruses into airway epithelial cells requires binding of a viral spike protein to a host cell receptor, followed by cleavage and activation of the viral spike protein mediated by the host cell. Without this cleavage, fusion of the viral and host cell membranes is blocked. The primary receptor for the human SARS-CoV-1 virus is angiotensin converting enzyme 2 (ACE2) (Li et al. 2003). The resultant complex is cleaved by the protease transmembrane protease serine 2 (TMPRSS2) (Shulla et al. 2011, Heurich et al. 2014). Therefore, active site inhibitors of these airway proteases could have broad therapeutic applicability against multiple respiratory viruses (Laporte & Naesens 2017). The approved drug camostat is a protease inhibitor that may block SARS-CoV-2 entry into cells by inhibiting the actions of TMPRSS2 (Kawase et al. 2012, Hoffmann et al. 2020). Nafamostat, another serine protease inhibitor, was found to be a potent inhibitor of S-mediated membrane fusion and blocked MERS-CoV infection in vitro (Yamamoto et al. 2016).

Otamixaban (FXV673), an anticoagulant, is a potent and selective direct inhibitor of coagulation factor Xa. Virtual docking studies suggest that otamixaban may bind to the serine protease TMPRSS2 (Rensi et al. 2020, preprint). Inhibition of TMPRSS2 is being examined for antiviral activity but its inhibitory potential and/or antiviral activity have not yet been determined so it is annotated here as a candidate drug. I-432 is another inhibitor of TMPRSS2 under investigation for anti viral potential (Pászti-Gere et al. 2016).
R-HSA-9681596 (Reactome) The rep proteases that are essential for viral polyprotein processing by the coronaviruses and enteroviruses exhibit a strong preference for substrates containing Gln at P1 position, and share an active-site conformation that engages the substrate's P1 residue. Compound 11r and compound 13b are peptidomimetic α-ketoamides that function as high-affinity non-cleavable substrate analogues and thus exhibit antiviral activity against dimeric 3C-like proteinases (C3Lp dimer) of coronaviruses and enteroviruses (Chen et al. 2005, Zhang et al. 2020). Their clinical safety and efficacy in COVID-19 are under investigation.
R-HSA-9681627 (Reactome) Human glycogen synthatse kinases GSK3A and GSK3B phosphorylate SARS-CoV-1 coronavirus N (nucleocapsid) protein on multiple serine and threonine residues. GSK3-mediated phosphorylation of the N protein is needed for efficient replication of viral genomic RNA (Wu et al. 2009).
R-HSA-9681651 (Reactome) nsp8 functions as an RNA-dependent RNA polymerase (RdRp) that serves as the primase for nsp12, the main RdRp of the SARS coronavirus 1 (SARS-CoV-1) (Imbert et al. 2006), as it is capable of de novo RNA synthesis (te Velthuis et al. 2011). nsp8 synthesizes short oligonucleotides (less than 6 bases long) using genomic RNA as a template. nsp8 requires at least one cytidine residue in the template sequence for its activity. Activity is dependent on manganese ions (Imbert et al. 2006). nsp8 can also extend primers but is 20-fold less efficient than nsp12 (te Velthuis et al. 2011).
R-HSA-9681674 (Reactome) Virally encoded RNA-dependent RNA polymerase (nsp12, also known as RdRP) is the key component of the replication transcription complex (RTC). As the human SARS coronavirus 1 (SARS-CoV-1) is a plus strand RNA virus, nsp12 first synthesizes the complementary minus RNA strand. The purified SARS-CoV-1 nsp12 shows both primer dependent and primer-independent RNA synthesis activities using homopolymeric RNA templates. The catalytic activity of nsp12 is strictly dependent on manganese ions (Mn2+) and primers when the template is a viral-genome-derived RNA representing part of the 3’-UTR of the plus strand with a polyA tail. A 36 nucleotide sequence from the 3’-UTR, predicted to form a stable stem-loop structure, seems to be the minimal cis-acting RNA element required for nsp12 to initiate RNA synthesis (Ahn et al. 2012). The complex of nsp7 and nsp8 confers processivity to nsp12 (Subissi et al. 2014).
R-HSA-9681840 (Reactome) After synthesizing the complementary minus RNA of the plus strand viral genomic RNA, virally encoded RNA-dependent RNA polymerase (nsp12, also known as RdRP) uses the minus strand as a template to generate viral genomic RNA that can be packaged into virions. Purified SARS-CoV-1 nsp12 shows both primer dependent and primer-independent RNA synthesis activity in vitro. nsp12 is able to initiate RNA synthesis with as little as 37 nucleotides of RNA from the 3’ end of the minus strand viral RNA (complementary to the 5’-UTR of the plus strand genomic RNA - c5’-UTR). Similar to the 3'-UTR of the plus strand, the 3' end of the minus strand (c5’-UTR) is predicted to form a stable stem-loop structure and seems to be the minimal cis-acting RNA element required for nsp12 to initiate RNA synthesis using the minus strand as a template (Ahn et al. 2012). It is unclear if replication of the minus strand is primer-dependent. The complex of nsp7 and nsp8 confers processivity to nsp12 (Subissi et al. 2014).
R-HSA-9682009 (Reactome) Human zinc finger CCHC-type and RNA-binding motif-containing protein 1 (ZCRB1, also known as MADP1) binds to the 5'UTR of the plus strand genomic RNA of the SARS-CoV-1, as well as other coronaviruses, infectious bronchitis virus (IBV) and human coronavirus OC43. ZCRB1 normally localizes to the nucleus, where it is a component of the U12-type spliceosome. Upon infection with a coronavirus, ZCRB1 appears in the cytosol. Binding of ZCRB1 to the 5'UTR stem of coronavirus genomic RNA is thought to be necessary for efficient transcription of viral genes (Tan et al. 2012).
R-HSA-9682258 (Reactome) Non-structural protein 14 (nsp14) of the human SARS coronavirus is a bifunctional enzyme bearing 3'-5 exoribonuclease activity involved in replication fidelity and RNA cap N7-guanine methyltransferase activity involved in 5'-RNA capping. nsp14 binds to the minimal replication and transcription complex (RTC), composed of nsp7, nsp8, and nsp12, by directly binding to nsp12 (the main RNA-dependent RNA polymerase). Binding of nsp14 does not affect the processivity of the RTC (Minskaia et al. 2006, Subissi et al. 2014).
R-HSA-9682465 (Reactome) The replication-transcription complex (RTC) completes synthesis of the genomic RNA complement (minus strand). The complex of nsp7 and nsp8 confers processivity to nsp12, the virally encoded RNA-dependent RNA polymerase that replicates the viral genomic RNA, enabling the RTC to complete the RNA synthesis with a very low dissociation rate. nsp7 plays a crucial role in maintaining binding of the RTC to the RNA. nsp14 subunit of the RTC does not affect the processivity (Subissi et al. 2014).
R-HSA-9682544 (Reactome) nsp10 forms a stable complex with nsp14 (Bouvet et al. 2012) and serves as a co-factor for nsp14, stimulating its 3'->5' exonuclease activity (Bouvet et al. 2012, Subissi et al. 2014, Bouvet et al. 2014).
R-HSA-9682563 (Reactome) In the presence of functional nsp14, which acts as a 3'-to-5' exonuclease, the mutation rate during human SARS coronavirus 1 (SARS-CoV-1) replication is 9 x 10^-7 (9E-7) per nucleotide per replication cycle or 2.2 x 10^-5 (2.2E-5) non-redundant substitutions per nucleotide, which translates into 2-3 nucleotide substitutions for each replicated SARS-CoV-1 genome. When nsp14 is defective, the mutation rate during SARS-CoV-1 replication increases to 1.2 x 10^-5 (1.2E-5) mutations per nucleotide per replication cycle or 3.34 x 10^-4 (3.34E-4) non-redundant substitutions per nucleotide, which translates into 12-23 nucleotide substitutions for each replicated SARS-CoV-1 genome (Eckerle et al. 2010). Here the process is annotated in two steps, nsp12- mediated misincorporation of a base (this reaction) and nsp14-mediated detection and removal of that base (next reaction).
R-HSA-9682603 (Reactome) nsp14 acts as 3'-5' exonuclease (Minskaia et al. 2006, Chen et al. 2007) that preferentially excises mismatched nucleotides from double stranded RNA (Minskaia et al. 2006, Bouvet et al. 2012). Binding to nsp10 increases the exonuclease activity of nsp14 (Bouvet et al. 2012, Subissi et al. 2014, Bouvet et al. 2014). nsp14 increases the fidelity of human SARS coronavirus 1 (SARS-CoV-1) replication by the nsp12 RNA-dependent RNA polymerase by 21-fold (Eckerle et al. 2010).
R-HSA-9682626 (Reactome) nsp13, which functions as the viral helicase, is as a part of the human SARS coronavirus 1 (SARS-CoV-1) replication-transcription complex (RTC), where it is directly bound to nsp12, the viral RNA-dependent RNA polymerase. nsp12 increases the helicase activity of nsp13 (von Brunn et al. 2007, Adedeji et al. 2012, Jia et al. 2019).
R-HSA-9682631 (Reactome) nsp13, the helicase of the human SARS coronavirus 1 (SARS-CoV-1) binds to DDX5, a host protein implicated in transcription, pre-mRNA processing, RNA degradation, RNA export, ribosome assembly and translation. DDX5 knockdown inhibits viral replication (Chen et al. 2009).
R-HSA-9682695 (Reactome) nsp13 is an ATP-dependent human SARS coronavirus 1 (SARS-CoV-1) helicase that functions in the 5'-3' direction to unwind double stranded RNAs that have a 5' single strand overhang at least 20 nucleotides long. nsp13 can also act on double strand DNA in vitro, but dsRNA is thought to be its physiological substrate. The catalytic activity of nsp13 is increased in the presence of nsp12, the viral RNA-dependent RNA polymerase. nsp13 is needed for the replication of SARS-CoV-1 and is thought to act by melting secondary structures in the genomic RNA template during replication, and also to be involved in unwinding of RNA duplexes during transcription of viral genes. nsp13 is a promising target for experimental anti-SARS-CoV-1 drugs (Tanner et al. 2003, Ivanov et al. 2004, Bernini et al. 2006, Chen et al. 2009, Lee et al. 2010, Adedeji et al. 2012).
R-HSA-9682712 (Reactome) Human SARS coronavirus 1 (SARS-CoV-1) non-structural protein 15 (nsp15) contains the LXCXE/D motif characteristic of proteins that bind to the retinoblastoma protein RB1. Binding to human RB1 increases the endonuclease activity of nsp15 but is not required for it. RB1 bound to nsp15 is retained in the cytosol. Interaction of nsp15 with RB1 likely affects the cell cycle of infected cells and probably modulates cytotoxicity of SARS-CoV-1 (Bhardwaj et al. 2012).
R-HSA-9682718 (Reactome) nsp15 forms a hexamer. Hexamer formation is necessary for the endonuclease activity of nsp15. nsp15 preferentially cleaves 3' of uridines, generating 2'-3' cyclic phosphates after cleavage. nsp15 requires Mn2+ ions for catalytic activity. C-terminal domain contains the active site, which faces away from the center of the hexamer and contains the extreme C-terminal residues. The middle and the N-terminal domains form extensive contacts with the other subunits of the hexamer. While the hexamer is likely formed by two asymmetric trimers, a trimer is not a stable intermediate. The catalytic pocket of nsp15 resembles the catalytic pocket of RNase A and their mechanism of endoribonuclease action is likely the same. Functional nsp15 is needed for production of viable virions. nsp15 is a genetic marker of the order Nidovirales, which includes the family Coronaviridae, as it is not present in other RNA viruses (Guarino et al. 2005, Ricagno et al. 2006, Bhardwaj et al. 2006, Joseph et al. 2007, Bhardwaj et al. 2008, Bhardwaj et al. 2012).
R-HSA-9683393 (Reactome) Nonstructural protein 15 (nsp15) of the SARS coronavirus (SARS-CoV-1) binds to the replication-transcription complex (RTC) through interaction with nsp8 (Imbert et al. 2008). This interaction appears to be conserved in other coronaviruses, such as mouse hepatitis virus (MHV) (Athmer et al. 2017). nsp15 is an endonuclease characteristic for the order Nidovirales that includes the family Coronaviridae. nsp15 preferentially cleaves 3' of uridines, generating 2'-3' cyclic phosphates after cleavage. nsp15 requires Mn2+ ions for catalytic activity. Functional nsp15 is needed for production of viable virions and for viral transcription (Guarino et al. 2005, Ricagno et al. 2006, Bhardwaj et al. 2006, Joseph et al. 2007, Bhardwaj et al. 2008, Bhardwaj et al. 2012). The biological role of nsp15 has not been elucidated. It may degrade host mRNAs to shut down host translation, but so far no human or viral RNA targets have been identified.
R-HSA-9683429 (Reactome) The non-structural protein 16 (nsp16) of the human SARS coronavirus is an AdoMet-dependent (nucleoside-2'O)-methyltransferase involved in capping of viral RNAs. nsp16 binds to nsp10, which serves as a cofactor for nsp16 (Bouvet et al. 2010, Lugari et al. 2010). Nsp16 alone is unstable and exhibits 2'-O-methyltransferase activity only in complex with nsp10 (Debarnot et al, 2011; Decroly et al, 2011). nsp10-mediated activation of nsp16 catalytic activity is conserved in all coronaviruses (Wang et al. 2015). The same binding surface of nsp10 interacts with nsp14 and nsp16, suggesting that binding of nsp14 and nsp16 to nsp10 is mutually exclusive. However, as nsp10 is produced in a higher number of copies than nsp14 and nsp16, and as nsp14 and nsp16 act coordinately in RNA capping, it is most likely that nsp14:nsp10 and nsp16:nsp10 complexes co-exist within the viral replication-transcription complex (RTC) (Bouvet et al. 2012, Bouvet et al. 2014). One structural study reported that nsp10 forms dodecamers (Su et al. 2006), which would potentially allow simultaneous binding of nsp14 and nsp16 to nsp10 homomeric complexes, but it is not certain if such homomeric complexes of nsp10 exist in vivo, and if the structure of the nsp10 dodecamer would be permissive for nsp16 binding (Chen et al. 2011). nsp10 contains two zinc fingers which are thought to be involved in RNA binding (Su et al. 2006, Joseph et al. 2006).
R-HSA-9683455 (Reactome) Human von Hippel Lindau (VHL) protein, a tumor suppressor that acts as a component of an E3 ubiquitin ligase complex, interacts with the non-structural protein 16 (nsp16) of the human SARS coronavirus 1 (SARS-CoV-1) and the mouse hepatitis virus, also a coronavirus. VHL negatively regulates SARS-CoV-1 replication, but the exact mechanism is not known (Yu et al. 2015).
R-HSA-9683467 (Reactome) Chloroquine (CQ) and hydroxychloroquine (HCQ) are diprotic weak bases that can exist in both protonated and unprotonated forms. Unprotonated CQ or HCQ can diffuse freely and rapidly across the membranes of cells and organelles to acidic cytoplasmic vesicles (late endosomes and lysosomes). Agents that have this ability are known as lysosomotropic agents. Once protonated, CQ2+ or HCQ2+ are trapped in the acidic lumen of these vesicles. This leads to an irreversible accumulation of CQ or HCQ in acidic vesicles to concentrations as much as 100 fold over cytosolic ones and to an elevation of vesicle pH due to trapping of H+ ions by CQ or HCQ. Thus, CQ analogues interfere with endosomal and lysosomal acidification, which in turn inhibits proteolysis, chemotaxis, phagocytosis and antigen presentation. As a result, cells are not able to proceed with endocytosis, exosome release and phagolysosomal fusion in an orderly manner (Foley & Tilley 1998, Yang & Shen 2020). In vitro, these endosomal acidification fusion inhibitors block cellular infection by a clinical isolate of SARS-CoV-2 (Wang et al. 2020, Hu et al. 2020).
R-HSA-9683478 (Reactome) Unprotonated chloroquine (CQ) and hydroxychloroquine (HCQ) can both diffuse freely and rapidly across the membranes of cells and organelles (Chinappi et al. 2010).
R-HSA-9683606 (Reactome) A certain part of the nucleoprotein can be found in the nucleolus. This localisation seems to depend on the protein's sumoylation (Li et al, 2005).
R-HSA-9683618 (Reactome) There is a mixed population of mRNA3 clones having six, seven, eight and nine T stretches located 14 nt downstream of the initiation codon that occur in vivo. The transcribed Us practically act as slippery sequences in heterogenous ORFs. Translation efficiency is reduced in slipping clones, however (Thiel et al, 2003; Tan et al, 2005; Wang et al, 2006).
R-HSA-9683622 (Reactome) SARS-CoV-1 mRNA5 has a length of 666 nt and encodes the 221 aa preprotein M (Thiel et al, 2003).
R-HSA-9683624 (Reactome) SARS-CoV-1 mRNA2 has a length of 3767 nt and encodes the 1255 aa spike preprotein (Thiel et al, 2003).
R-HSA-9683630 (Reactome) Some phosphorylated N is found to associate with the cell membrane (Surjit et al, 2005).
R-HSA-9683634 (Reactome) Nucleoprotein is capable of homodimerization in a mammalian cellular environment. It may also oligomerise transiently which is a prerequisite to forming the capsid of SARS-CoV (Surjit et al, 2004; Li et al, 2005; Chang et al, 2013).
R-HSA-9683635 (Reactome) Both a predicted beta-hairpin motif and the N-terminal part of SARS-Cov protein E are sufficient for its localization to the Golgi membrane. Although porin activity has been shown for protein E it cannot be detected in the plasma membrane of infected cells (Liao et al, 2006; Cohen et al, 2011; Nieto-Torres, 2011).
R-HSA-9683648 (Reactome) In the cis- to medial Golgis, conversion of high-mannose to complex type N-glycans side chains of Spike occurs. The N-acetylglucosaminyltransferase called GlcNAc-TI (MGAT1) adds a GlcNAc residue in the core of some high-mannose chains (Ritchie et al, 2010; Nal et al, 2005, Song et al, 2004).
R-HSA-9683653 (Reactome) Two of the four cysteine-rich clusters of the SARS-CoV-1 spike protein are modified by palmitoylation. This is required for the protein's partitioning into detergent-resistant membranes and for cell–cell fusion. In general, palmitoylation is usually non-enzymatic (Petit et al, 2007; McBride and Machamer, 2010; Veit, 2012).
R-HSA-9683656 (Reactome) SARS-CoV-1 mRNA4 has a length of 231 nt and encodes the 76 aa preprotein E (Thiel et al, 2003).
R-HSA-9683663 (Reactome) N-glycan side chains on the nascent SARS-CoV-1 spike protein get their terminal glucose moieties cleaved by ER glucosidases I and II, before folding. Iminosugars inhibit this process and are good candidates for broad-spectrum anivirals (Zhao et al, 2015).
R-HSA-9683664 (Reactome) The majority of nucleoprotein is serine-phosphorylated in the cytosol and, possibly, in the nucleus where it gets immediately transported to the cytosol. Phosphorylation is catalyzed by glycogen synthase kinase 3 (GSK3) and several other host cell kinases (Surjit et al, 2005; Wu et al. 2009).
R-HSA-9683669 (Reactome) A minor proportion of the SARS-CoV E protein is modified by N-linked glycosylation at the N66 residue. This variant appears to be more likely to form multimers, and it shows a different membrane topology than the main variant (Yuan et al, 2006).
R-HSA-9683670 (Reactome) Protein E forms a pentamer of monomers without disulfide bonds (Parthasarathy et al, 2012).
R-HSA-9683679 (Reactome) SARS-CoV E protein is ubiquitinated both in vitro and in cells (Alvarez et al, 2011).
R-HSA-9683687 (Reactome) Lysine-62 is the major sumoylation site of N protein. Abolition of sumoylation of nucleoprotein significantly decreases homo-oligomerisation of the protein (Li et al, 2005)
R-HSA-9683712 (Reactome) Viral protein 3a translocates from the cytosol to the ERGIC (endoplasmic reticulum Golgi intermediate compartment) (Oostra et al. 2006).
R-HSA-9683714 (Reactome) Significant amounts of the unphosphorylated N protein are associated with the cell membrane (Surjit et al, 2005).
R-HSA-9683718 (Reactome) Protein M accumulates in the Golgi complex and recruits Spike protein to the sites of virus assembly and budding in the ERGIC (Voss et al, 2009).
R-HSA-9683719 (Reactome) The SARS-Cov spike protein forms a homotrimer that is not disullfide-linked (Song et al, 2004).
R-HSA-9683720 (Reactome) SARS-CoV E protein is modified by palmitoylation at all three cysteine residues. In general, palmitoylation is usually non-enzymatic (Liao et al, 2006, Veit, 2012).
R-HSA-9683734 (Reactome) Protein M accumulates in the Golgi complex and recruits Spike protein to the sites of virus assembly and budding in the ERGIC (Voss et al, 2009).
R-HSA-9683735 (Reactome) SARS-CoV-1 mRNA9a has a length of 1269 nt and encodes the 422 aa pre-nucleoprotein, the most abundant viral protein expressed during infection. Nucleoprotein is translated by cytosolic free ribosomes and most of it stays in the cytosol where it soon colocalizes with nsp3 and viral genomic RNA. It is involved in replication and transcription of the viral genome, but it is also a structural component of the virion (Thiel et al, 2003; Li et al, 2005; Stertz et al, 2007; Fung & Liu, 2019).
R-HSA-9683746 (Reactome) Protein 3a can form homodimers and tetramers. The homotetramer shows typical patterns of ion channels. Transport of potassium ions through this channel is effective (Lu et al, 2006). Potassium efflux by protein 3a is important for 3a-induced NLRP3 inflammasome activation (Chen et al, 2019).
R-HSA-9683751 (Reactome) Protein M is exclusively N-glycosylated at asparagine 4 by an unknown glycosyltransferase. However, further processing of N-linked glycans is prevented in SARS-CoV-infected cells. Both the glycosylated and nonglycosylated M is incorporated into the virion. In summary, glycosylation of M is neither a prerequisite for intra-cellular transport nor for recruitment into the virion (Voss et al, 2006).
R-HSA-9683755 (Reactome) Glycosyltransferases in the endoplasmatic reticulum are responsible for the attachment of numerous high-mannose N-glycans on the SARS-CoV-1 spike protein. After virion assembly and release these glycosidations are required for fusion with host cells (Krokhin et al, 2003; Nal et al, 2005; Ritchie et al, 2010).
R-HSA-9683760 (Reactome) A sialyltransferase adds a terminal sialic acid moiety to protein 3a with an O-linked glycosyl side chain. This glycosylated form later is associated with the virion (Oostra et al, 2006).
R-HSA-9683764 (Reactome) Trimmed palmitoylated Spike protein trimers become associated with the ERGIC (ER-Golgi Intermediate Compartment) (Fung & Liu 2019).
R-HSA-9683765 (Reactome) As early as 3 hours post-infection, cytoplasmic accumulations of N are formed in infected cells, they colocalize with viral RNA. From 5 hours post-infection on, N can be detected in the Golgi, the budding site (Stertz et al, 2007).
R-HSA-9683769 (Reactome) A sialyltransferase adds a terminal sialic acid moiety to protein 3a with an O-linked glycosyl side chain. This glycosylated form later is associated with the virion (Oostra et al, 2006).
R-HSA-9683772 (Reactome) Calnexin transiently binds the unfolded spike protein and prevents its aggregation and premature degradation, ensuring its correct folding (Fukushi et al, 2012)
R-HSA-9684016 (Reactome) The genomic and subgenomic (sg) mRNAs of SARS-CoV-1 coronavirus are presumed to be capped at their 5′ end, based on studies of the mouse hepatitis virus (MHV) (Lai and Stohlman 1981) and the equine torovirus (van Vliet et al. 2002). Non-structural protein 14 (nsp14) acts as an RNA guanine-N7-methyltransferase (N7-MTase) that completes the synthesis of the cap-0 on SARS-CoV-1 mRNAs. The cap-0 represents N7-methyl guanosine connected to the 5′ nucleotide through a 5′ to 5′ triphosphate linkage, and is also known as m7G cap or m7Gppp cap. The N7-MTase domain maps to the carboxy-terminal part of nsp14 (Chen et al. 2009). Cap-0 formation requires three sequential reactions catalyzed by RNA triphosphatase (TPase), guanylyltransferase (GTase), and N7-MTase. There is no evidence that nsp14 possesses TPase and GTase activities, and no other SARS-CoV-1 proteins with these activities have been identified, so the identities of the enzymes that mediate these required steps remain unknown. Based on the study of the human coronavirus 229E, non-structural protein 13 (nsp13) may have a TPase activity in addition to its established helicase activity (Ivanov and Ziebuhr 2004).
R-HSA-9684017 (Reactome) The genomic and subgenomic mRNAs of SARS-CoV-1 coronavirus, including the plus strand genomic RNA, are presumed to be capped at their 5′ end, based on studies of the mouse hepatitis virus (MHV) (Lai and Stohlman 1981) and the equine torovirus (van Vliet et al. 2002). Non-structural protein 14 (nsp14) acts as an RNA guanine-N7-methyltransferase (N7-MTase) that completes the synthesis of the cap-0 on the SARS-CoV-1 plus strand genomic RNA. Cap-0 represents N7-methyl guanosine connected to the 5′ nucleotide through a 5′ to 5′ triphosphate linkage, and is also known as m7G cap or m7Gppp cap. The N7-MTase domain maps to the carboxy-terminal part of nsp14 (Chen et al. 2009). Cap-0 formation requires three sequential reactions catalyzed by RNA triphosphatase (TPase), guanylyltransferase (GTase), and N7-MTase. There is no evidence that nsp14 possesses TPase and GTase activities, and no other SARS-CoV-1 proteins with these activities have been identified, so the identities of the enzymes that mediate these required steps remain unknown. Based on the study of the human coronavirus 229E, non-structural protein 13 (nsp13) may have a TPase activity in addition to its established helicase activity (Ivanov and Ziebuhr 2004).
R-HSA-9684018 (Reactome) The genomic and subgenomic mRNAs of SARS-CoV-1 coronavirus, including the minus strand genomic RNA complement, are presumed to be capped at their 5′ end, based on studies of the mouse hepatitis virus (MHV) (Lai and Stohlman 1981) and the equine torovirus (van Vliet et al. 2002). The non-structural protein 14 (nsp14) acts as an RNA guanine-N7-methyltransferase (N7-MTase) that completes the synthesis of the cap-0 on SARS-CoV-1 minus strand genomic RNA. The cap-0 represents N7-methyl guanosine connected to the 5′ nucleotide through a 5′ to 5′ triphosphate linkage, and is also known as m7G cap or m7Gppp cap. The N7-MTase domain maps to the carboxy-terminal part of nsp14 (Chen et al. 2009). Cap-0 formation requires three sequential reactions catalyzed by RNA triphosphatase (TPase), guanylyltransferase (GTase), and N7-MTase. There is no evidence that nsp14 possesses TPase and GTase activities, and no other SARS-CoV-1 proteins with these activities have been identified, so the identities of the enzymes that mediate these required steps remain unknown. Based on the study of the human coronavirus 229E, non-structural protein 13 (nsp13) may have a TPase activity in addition to its established helicase activity (Ivanov and Ziebuhr 2004).
R-HSA-9684030 (Reactome) The genomic and subgenomic mRNAs of SARS-CoV-1 coronavirus, including the minus strand genomic RNA, are presumed to be capped at their 5′ end, based on studies of the mouse hepatitis virus (MHV) (Lai and Stohlman 1981) and the equine torovirus (van Vliet et al. 2002). Non-structural protein 16 (nsp16) acts as a 2'O-methyltransferase that converts coronavirus cap-0 to cap-1, which was first demonstrated with nsp16 cloned from the feline coronavirus (FCV) (Decroly et al. 2008). Cap-0 represents N7-methyl guanosine connected to the 5′ nucleotide through a 5′ to 5′ triphosphate linkage (also known as m7G cap or m7Gppp cap). Cap-1 is generated by an additional methylation on the 2′O position of the initiating nucleotide, and is also known as m7GpppNm. Non-structural protein 10 (nsp10) acts as an activator of nsp16 and is necessary for cap-1 synthesis (Bouvet et al. 2010, Decroly et al. 2011). Coronavirus RNAs with cap-1 are protected from IFIT-mediated interferon response. IFITs are interferon-induced proteins with tetratricopeptide repeats that recognize unmethylated 2'-O RNAs and act to inhibit expression of virally encoded mRNAs (Menachery et al. 2014).
R-HSA-9684032 (Reactome) The genomic and subgenomic mRNAs of SARS-CoV-1 coronavirus, including the plus strand genomic RNA, are presumed to be capped at their 5′ end, based on studies of the mouse hepatitis virus (MHV) (Lai and Stohlman 1981) and the equine torovirus (van Vliet et al. 2002). The non-structural protein 16 (nsp16) acts as a 2'O-methyltransferase that converts coronavirus cap-0 to cap-1, which was first demonstrated with nsp16 cloned from the feline coronavirus (FCV) (Decroly et al. 2008). Cap-0 represents N7-methyl guanosine connected to the 5′ nucleotide through a 5′ to 5′ triphosphate linkage (also known as m7G cap or m7Gppp cap). Cap-1 is generated by an additional methylation on the 2′O position of the initiating nucleotide, and is also known as m7GpppNm. Non-structural protein 10 (nsp10) acts as an activator of nsp16 and is necessary for cap-1 synthesis (Bouvet et al. 2010, Decroly et al. 2011). Coronavirus RNAs with cap-1 are protected from IFIT-mediated interferon response, as IFITs recognize unmethylated 2'-O RNAs. IFITs are interferon-induced proteins with tetratricopeptide repeats that recognize unmethylated 2'-O RNAs and act to inhibit expression of virally encoded mRNAs (Menachery et al. 2014).
R-HSA-9684033 (Reactome) The subgenomic mRNAs of SARS-CoV-1 coronavirus are presumed to be capped at their 5′ ends, based on studies of the mouse hepatitis virus (MHV) (Lai and Stohlman 1981) and the equine torovirus (van Vliet et al. 2002). The non-structural protein 16 (nsp16) acts as a 2'O-methyltransferase that converts coronavirus cap-0 to cap-1, which was first demonstrated with nsp16 cloned from the feline coronavirus (FCV) (Decroly et al. 2008). Cap-0 represents N7-methyl guanosine connected to the 5′ nucleotide through a 5′ to 5′ triphosphate linkage (also known as m7G cap or m7Gppp cap). Cap-1 is generated by an additional methylation on the 2′O position of the initiating nucleotide, and is also known as m7GpppNm. The non-structural protein 10 (nsp10) acts as an activator of nsp16 and is necessary for cap-1 synthesis (Bouvet et al. 2010, Decroly et al. 2011). Coronavirus RNAs with cap-1 are protected from IFIT-mediated interferon response, as IFITs recognize unmethylated 2'-O RNAs. IFITs are interferon-induced proteins with tetratricopeptide repeats that recognize unmethylated 2'-O RNAs and act to inhibit expression of virally encoded mRNAs (Menachery et al. 2014).
R-HSA-9684218 (Reactome) M protein is the most abundant component of the mature virionm and contributes to the shape of the virus. It consists of three transmembrane domains with an N-terminus outside the virus and an internal C-terminus (N-exo, C-endo conformation). Homotypic interactions between M proteins contribute to the initial formation of a nascent virus by forming a lattice, consistent with what is seen in other coronavirus systems (Tseng et al, 2010; de Hann et al, 1998; de Haan et al, 2000; Locker et al, 1995). Multiple segments of M are required for oligomerization (Tseng et al, 2010; de Hann et al, 1998; de Haan et al, 2000; reviewed in Masters, 2006). Both glycosylated and non-glycosylated forms of M are incorporated into the virion, and the significance of the N-linked glycosylation is not clear (Voss et al, 2006; Voss et al, 2009).
Despite its importance, expression of M alone is not sufficient to drive formation of a mature virus (reviewed in Masters, 2006). Protein-protein interactions between M and S, N and E, among other components, are required for assembly of a mature virus and for membrane curvature. Many studies have examined the minimal system required for release of viral like particles (VLPs) with sometimes contradictory results, but interactions between M, N and E are sufficient to promote release of significant numbers of VLPs (Ho et al, 2004; Huang et al, 2004; Mortola and Roy, 2004; Hsieh et al, 2005; Siu et al, 2008; Hatakeyama et al, 2008; Tseng et al, 2013; reviewed in Masters, 2006)
R-HSA-9684229 (Reactome) N protein is synthesized in the cytosol of the host cell and then moves adjacent to the endoplasmic reticulum-Golgi intermediate compartment (ERGIC) membrane, where mature virions are assembled. The primary function of the SARS-CoV nucleocapsid (N) protein is to encapsulate the positive-strand 5'-capped genomic RNA into a nucleocapsid for export. Nucleocapsid formation is depends on multiple weak protein-protein and protein-RNA interactions (reviewed in Chang et al, 2014).
The SARS-CoV N protein has globular N-terminal and C-terminal domains separated by three intrinsically disordered regions (IDRs) (Chang et al, 2006; Chang et al, 2009). N protein forms a weak dimer in the absence of RNA mediated by residues in the middle and C-terminal IDR (He et al, 2004a; Luo et al, 2006; Chang et al, 2005; Surjit et al, 2004; Yu et al, 2005; Chang et al, 2006; Chang et al, 2013; Surjit and Lal, 2008). Positive residues in the middle IDR are subject to phosphorylation, which may affect the function of N (Surjit et al, 2005; Peng et al, 2008).
Binding of the genomic RNA to one or a small number of N-N dimers may be the initiating event in nucleocapsid formation. Both the NTD and the CTD of N have been shown to have RNA-binding activity (Huang et al, 2004a; Huang et al, 2004b; Chen et al, 2007; Chang et al, 2009; Takeda et al, 2008), and the IDRs seem likely to also contribute (Chang et al, 2009). These initial binding events may nucleate nucleocapsid formation through further recruitment of N protein dimers (reviewed in Chang et al, 2014).
R-HSA-9684234 (Reactome) The final ribonucleoprotein complex is a hollow helical structure with an approximate diameter of 9-16nm, with the C-terminal domain of N protein forming the inner core and the N-terminal domain forming the outer surface (Neuman et al, 2006; Chen et al, 2007). Oliomerization of the N protein capsid coat is likely nucleated through both protein-RNA and protein-protein interactions by the first few N-protein dimers on the genomic RNA (Saikatendu et al, 2007; Chang et al, 2013; reviewed in Chang et al, 2014). Each N dimer may make contact with up to 7 bases of the RNA (reviewed in Chang et al, 2014).
R-HSA-9684238 (Reactome) Formation of an M lattice nucleates recruitment of other structural proteins including N, E and S (reviewed in Masters, 2006; Fung and Liu, 2019; Ujike and Taguchi, 2015). Expression of M and N or M and E have been shown to be sufficient to support release of viral like particles (VLPs), with co-expression of all three promoting release of significant numbers of VLPs (Huang et al, 2004; Ho et al, 2004; Hsieh et al, 2005; Mortola and Roy, 2004; Siu et al, 2008). Neither the S protein nor the genomic RNA are required for release of these otherwise morphologically normal particles, but both are incorporated if co-expressed (Siu et al, 2008).
E protein is a small, integral membrane protein that is present in low amounts in the mature virion. It forms homo-oligomers and may exist as a homopentamer (Torres et al, 2005). E is palmitoylated and N-glycosylated, although the significance of these modifications is not clear (Liao et al, 2006; Yuan et al, 2006). E is recruited to the M lattice through interactions between the transmembrane domains of both proteins, and plays multiple roles in virion assembly and host interactions, including membrane budding, induction of apoptosis and membrane permeability (Hsieh et al, 2008; Chen et al, 2009; reviewed in Schoeman and Fielding, 2019; Liu et al, 2016).
The ribonucleoprotein complex is recruited to the assembling virion through interactions with the M C-terminal tail, and appears to be independent of viral RNA (Hsieh et al, 2008; Hatakeyama et al, 2008; He et al, 2004; Luo et al, 2006; reviewed in Ujike and Taguchi, 2015).
R-HSA-9684241 (Reactome) S trimers are recruited to the assembling virion through interaction with M protein (reviewed in Ujike and Taguchi, 2015). Multiple regions of M contribute to the recruitment of S, with a single tyrosine residue in the C-terminal domain of M playing a critical role (McBride et al, 2010a; Hsieh et al, 2008). Interaction with M is aided by a dibasic motif in the C-terminus of S, which promotes retrieval of the spike protein from the cell surface by binding the COPI coat (McBride et al, 2007; Ujike et al, 2016). Palmitoylation of the C-terminus of S appears dispensible for the interaction with M in SARS-COV-1, unlike the case in other coronaviruses (Ujike et al, 2012; McBride 2010b; reviewed in Ujike and Taguchi, 2015). Size estimates and modelling suggest the mature virion has approximately 300 S trimers (Neuman et al, 2006; reviewed in Chang et al, 2014).
R-HSA-9684261 (Reactome) Part of nsp4 protein becomes N-glycosylated and gets recruited to the replication complexes in infected cells (Oostra et al, 2007)
R-HSA-9684273 (Reactome) Main protease cleaves all cleavage sites of pp1a and ppa1b starting with nsp4/5, thus cleaving itself, and all the cytosolic RTC proteins (Fan et al, 2004)
R-HSA-9684275 (Reactome) To process the nsp3/4 cleavage site, PL-PRO and, presumably, nsp3-4 need to be glycosylated and localized to a membrane (Harcourt et al, 2004)
R-HSA-9684277 (Reactome) In about 15% of translation attempts of the genomic viral mRNA1 in the host cell cytosol, a -1 frameshift happens after the nsp10 gene that leads to translation of the full 7,033 aa pp1ab polyprotein (Baranov et al, 2005).
R-HSA-9684282 (Reactome) Formation of the nsp9 dimer is necessary for viral viabilit. While the dimer retains only a slight advantage over the monomer in RNA binding the nsp9 monomer does not function in vivo, probably because of the correct positioning of RNA in the replication complex requiring a properly dimerized nsp9 (Miknis et al, 2009)0
R-HSA-9684290 (Reactome) To process the nsp3/4 cleavage site, PL-PRO and, presumably, nsp3-4 need to be glycosylated and localized to a membrane (Harcourt et al, 2004)
R-HSA-9684301 (Reactome) In most translation attempts the genomic viral mRNA1 in the cytosol is translated to a shortened polyprotein, pp1a (4,382 aa), that does not contain genome replication enzymes (Baranov et al, 2005).
R-HSA-9684309 (Reactome) Main protease cleaves all cleavage sites of pp1a and ppa1b starting with nsp4/5, thus cleaving itself, and all the cytosolic RTC proteins (Fan et al, 2004)
R-HSA-9684321 (Reactome) Glycosylated nsp3 (papain-like protease) cleaves the N-proximal polyprotein regions at three sites (Thiel et al, 2003; Harcourt et al, 2004)
R-HSA-9684323 (Reactome) The main protease has no post-translational modifications. Most of it is in monomeric form, but only the dimer shows cysteine endopeptidase activity (Sun et al, 2003; Fan et al, 2004)
R-HSA-9684336 (Reactome) The papain-like protease domain of the nsp1-4 fragment alone is sufficient for processing the nsp1/2 and nsp2/3 cleavage sites (Harcourt et al, 2004)
R-HSA-9684340 (Reactome) Main protease cleaves all cleavage sites of pp1a and ppa1b starting with nsp4/5, thus cleaving itself, and all the cytosolic RTC proteins (Fan et al, 2004)
R-HSA-9684350 (Reactome) In the host cell cytosol the pp1a polyprotein spontaneously dimerizes. This temporary dimer has weak protease activity (Chen et al, 2010).
R-HSA-9684351 (Reactome) The crucial step of autocleavage of pp1a involves the formation of an "intermediate" pp1a dimer which has weak protease activity. This "embedded" 3CLp liberates itself by cleaving the ends off its monomer in trans. Only after that the cleaved 3CLp forms a dimer, the most efficient form of the enzyme (Hsu et al, 2005; Chen et al, 2010; Muramatsu et al, 2016).
R-HSA-9684352 (Reactome) To process the nsp3/4 cleavage site, PL-PRO and, presumably, nsp3-4 need to be glycosylated and localized to a membrane (Harcourt et al, 2004)
R-HSA-9685519 (Reactome) SARS-CoV-1 plus strand genomic RNA, like genomic RNAs of other coronaviruses, possesses a polyadenylation signal in its 3'UTR and is polyadenylated by an undetermined viral RNA polymerase, possibly nsp8 or nsp12 (Spagnolo and Hogue 2000, Peng et al. 2016, Tvarogova et al. 2019).
R-HSA-9685531 (Reactome) Interaction of the ribonucleocapsid and the structural proteins in the ERGIC membrane promotes the formation of virions by budding into to the ERGIC lumen (reviewed in Masters, 2006). Coronavirus membrane curvature is driven by M lattice formation, interaction with the nucleocapsid and by E protein (de Haan et al, 1998; de Haan et al, 2000; Hsieh et al, 2005; Hsieh et al, 2008; reviewed in Masters, 2006; Ujike and Taguchi, 2015; Schoeman and Fielding 2019).
R-HSA-9685542 (Reactome) Similar to other coronaviruses, SARS-CoV-1 virions are released from the host cell by exocytosis in smooth-walled vesicles (reviewed in Ujike and Taguchi, 2015; Masters, 2006; Fung and Liu, 2019). The nature and details of this export remain to be elucidated.
R-HSA-9685597 (Reactome) After synthesizing the complementary minus RNA of the plus strand viral genomic RNA, SARS-CoV-1 replication-transcription complex (RTC) associates with the minus strand to initiate plus strand synthesis and to initiate transcription of subgenomic (sg) mRNAs (Ahn et al. 2012).
R-HSA-9685639 (Reactome) SARS-CoV-1 encodes eight subgenomic RNAs, mRNA2 to mRNA9. mRNA1 corresponds to the genomic RNA. The 5' and 3' ends of subgenomic RNAs are identical, in accordance with the template switch model of coronavirus RNA transcription (Snijder et al. 2003, Thiel et al. 2003, Yount et al. 2003). Therefore, consistent with this and the studies of the murine hepatitis virus (MHV), which is closely related to SARS-CoV-1, genomic positive strand RNA is first transcribed into negative sense (minus strand) subgenomic mRNAs, that subsequently serve as templates for the synthesis of positive strand subgenomic mRNAs. Negative-sense virus RNAs are present in much smaller amounts than positive-sense RNAs (Irigoyen et al. 2016). Each subgenomic RNA contains a leader transcription regulatory sequence (leader TRS) that is identical to the leader of the genome, appended via polymerase “jumping� during negative strand synthesis to the body transcription regulatory sequence (body TRS), a short, AU-rich motif of about 10 nucleotides found upstream of each ORF that is destined to become 5' proximal in one of the subgenome-length mRNAs. The 3' and 5'UTRs may interact through RNA–RNA and/or RNA–protein plus protein–protein interactions to promote circularization of the coronavirus genome, placing the elongating minus strand in a favorable topology for leader-body joining. The host protein PABP was found to bind to the coronavirus 3' poly(A) tail and to interact with the host protein eIF-4G, a component of the three-subunit complex that binds to mRNA cap structures, which may promote the circularization of the coronavirus genome. Two viral proteins that bind to the coronavirus 5'UTR, the N protein and nsp1, may play a role in template switching. The poly(A) tail is necessary for the initiation of minus-strand RNA synthesis at the 3' end of genomic RNA. For review, please refer to Sawicki et al. 2007 and Yang and Leibowitz 2015.
R-HSA-9685655 (Reactome) Lysosomes play critical roles in human biology receiving, trafficking, processing, and degrading biological molecules from cellular processes such as endocytosis, phagocytosis, autophagy and secretion. Lysosomes house around sixty proteolytic enzymes, among them cathepsins. Cathepsins are involved in many processes involving cell death, protein degradation, post-translational modifications of proteins, extracellular matrix (ECM) remodeling, autophagy, and immune signaling. The early stages of the viral life cycle involve the cleavage of the viral spike protein by cathepsin L (CTSL) in late endosomes, facilitating viral RNA release to continue viral replication. Teicoplanin, a glycopeptide antibiotic used to treat Gram-positive bacterial infection, especially in Staphylococcal infections, was shown to have efficacy in vitro against Ebola Virus, MERS and SARS-CoV-1 (Zhou et al. 2016).

Teicoplanin is thought to inhibit the low pH cleavage of the viral spike protein by CTSL in late endosomes thereby preventing the release of genomic viral RNA and the continuation of virus replication cycle (Baron et al. 2020). The target sequence that serve as the cleavage site for CTSL is conserved in the SARS-CoV-2 spike protein (Zhou et al. 2020 [preprint]). Further investigation is required to determine the therapeutic potential of teicoplanin in COVID-19 patients.

Relacatib is an investigational drug trialed for the treatment of osteoporosis (Duong et al. 2016). It is a potent CTSK inhibitor but also shows activity against CTSL (Kumar et al. 2007) so could potentially be investigated for Covid-19 patients. The antileprotic drug clofazimine and the antituberculous drugs rifampicin and isoniazid have been shown to inhibit cathepsins B, H and L from purified goat and bovine brains (Kamboj et al. 2003).
R-HSA-9685681 (Reactome) SARS-CoV-1 encodes eight subgenomic RNAs, mRNA2 to mRNA9. mRNA1 corresponds to the genomic RNA. mRNA2 encodes the S protein. mRNA3 is bicistronic and encodes proteins 3a and 3b. mRNA4 encodes the E protein. mRNA5 encodes the M protein. mRNA6 encodes the protein 6. mRNA7, mRNA8 and mRNA9 are bicistronic, with mRNA7 encoding proteins 7a and 7b, mRNA8 encoding proteins 8a and 8b, and mRNA 9 encoding proteins 9a and N. The 5' and 3' ends of subgenomic RNAs are identical, in accordance with the template switch model of coronavirus RNA transcription (Snijder et al. 2003, Thiel et al. 2003, Yount et al. 2003). Based on studies of the murine hepatitis virus (MHV), which is closely related to SARS-CoV-1, positive-sense virus mRNAs are present at much higher amounts than negative-sense mRNAs (Irigoyen et al. 2016).
R-HSA-9685906 (Reactome) SARS-CoV-1 plus strand subgenomic mRNAs share a 3'UTR with the plus strand genomic RNA, and as this 3'UTR possesses a polyadenylation signal, they undergo polyadenylation by an undetermined viral RNA polymerase, possibly nsp8 or nsp12 (Spagnolo and Hogue 2000, Peng et al. 2016, Tvarogova et al. 2019).
R-HSA-9685939 (Reactome) As it contains cargo sorting motifs in its cytoplasmic domain, protein 3a gets localized by the cell's protein transport system to the cell membrane where it functions as an ion channel (Tan et al, 2004). This ion channel function is necessary for the protein's pro-apoptotic function (Chan et al, 2009).
R-HSA-9685950 (Reactome) Protein 3a is rapidly internalized into cells by endocytosis. It contains a Yxxφ motif and also diacidic motifs which are typically found in internalized membrane proteins (Tan et al, 2004). The ability to be internalized is necessary for the protein's pro-apoptotic function (Wong et al, 2006; Chan et al, 2009).
R-HSA-9685956 (Reactome) Membranous structures containing protein 3a are being shedded from the cell membrane (Huang et al, 2006).
R-HSA-9686005 (Reactome) On the final assembly, proteomics data suggest that the NAB−βSM−TM1 domains of nsp3 can interact with nsp7 − 8, as well as nsps 12–16, and the domain Y1 plus CoV-Y interacts with nsp9 and nsp12 (Imbert et al., 2008). Also a PL2pro−NAB−βSM−TM1 construct of Nsp3 can bind Nsp4 and Nsp12, while the region from TM1 to the end of Nsp3 only binds Nsp8 (Pan et al., 2008).
R-HSA-9686013 (Reactome) The SARS-CoV nsp3 was shown to bind ORF7a and Nsp6 by using proteomics analysis (Neuman et al, 2008)
R-HSA-9686015 (Reactome) nsp3 and nsp4 alone caused considerable ER membrane deformation, producing a perinuclear double-walled maze-like body (MLB), and the nsp3–nsp4 interaction was shown to be absolutely necessary for such membrane rearrangement. Further necessary factors are nsp6 and unidentified host factors (Angelini et al 2013, Sakai et al 2017). nsp6 by itself can form Atg5 and LC3II-positive vesicles classically observed in autophagy (Cottam et al, 2014). However, in mouse hepatitis virus (MHV) infections, EDEM1 and OS9 of the ER-associated degradation system have been shown to be necessary co-factors (Reggiori et al, 2010).
R-HSA-9686061 (Reactome) Nucleoprotein (N) is ADP-ribosylated. The modification is maintained both in the cell and in virions (Grunewald et al, 2018). Members of the protein mono-ADP-ribosyltransferase (PARP) enzyme family are thought to catalyze this reaction (Fehr et al. 2020).
R-HSA-9686174 (Reactome) In addition to the main structural proteins and the nucleocapsid, the mature virion may also contain low proportions of accessory proteins, including protein 3a and 7a (reviewed in McBride and Fielding, 2012). Protein 3a has been shown to interact with E, M, S and protein 7a and is estimated to be present in the virion at 2/3 the molar ratio of E protein (Ito et al, 2005; Shen et al, 2005; Tan et al, 2004). Although 3a tetramers are predicted to act as ion channels in the host plasma membrane, increasing cell permeability, the role of 3a in the mature virion is not clear (Lu et al, 2006; reviewed in McBride and Fielding, 2012). Protein 7a is type 1 transmembrane protein that interacts with M, E, S and protein 3a and may be incorporated into the mature virion. What functional role protein 7a may play in the assembled virion is unclear (Huang et al, 2006; Fielding et al, 2004; Tan et al, 2004).
R-HSA-9686699 (Reactome) The SARS-CoV-1 nucleocapsid is released from the host cell endosome into the cytosol. Molecular details of this step are not well worked out. Studies of the infection of the human cultured cells with HCoV-229E coronavirus established a requirement for VCP (transitional endoplasmic reticulum ATPase) protein function for release to occur (Wong et al. 2015). A similar requirement for VCP involvement in SARS-CoV-1 nucleocapsid release is inferred here.
R-HSA-9686709 (Reactome) The viral nucleocapsid complex, released into the host cell cytosol, dissociates to release the viral RNA genome (Fung & Liu 2019).
R-HSA-9686710 (Reactome) Spike protein S1: attaches the virion to the cell membrane by interacting with host receptor, initiating the infection.


Spike protein S2: Acts as a viral fusion peptide which is unmasked following S2 cleavage occurring upon virus endocytosis. 


Spike protein S2: mediates fusion of the virion and cellular membranes by acting as a class I viral fusion protein. Under the current model, the protein has at least three conformational states: pre-fusion native state, pre-hairpin intermediate state, and post-fusion hairpin state. During viral and target cell membrane fusion, the coiled coil regions (heptad repeats) assume a trimer-of-hairpins structure, positioning the fusion peptide in close proximity to the C-terminal region of the ectodomain. The formation of this structure appears to drive apposition and subsequent fusion of viral and target cell membranes.

Within the host cell endocytic vesicle, SARS-CoV-1 Spike (S) protein is cleaved between residues 797 and 798 by cathepsin L1 (CTSL) (Huang et al. 2006). The roles of S protein in viral binding to the host cell membrane and fusion of viral and host cell membranes and thus the central role of S protein in determining the host range and tissue tropisms of the virus are reviewed by Belouzard et al. (2012).
R-HSA-9686711 (Reactome) SARS-CoV-1 virions attached to the host cell surface via a complex involving viral spike (S) protein and host angiotensin-converting enzyme 2 (ACE2) undergo endocytosis. Studies with pseudoviruses have established that S protein is necessary and sufficient for mediating viral attachment and entry. Inhibition of this SARS-CoV-1 S protein-mediated transduction by two different classes of lysosomotropic agents in multiple cell lines strongly suggests that acidification of endosomes is needed for viral entry (Hofmann et al. 2004; Simmons et al. 2004; Yang et al. 2004). The roles of S protein in viral binding to the host cell membrane and fusion of viral and host cell membranes and thus the central role of S protein in determining the host range and tissue tropisms of the virus are reviewed by Belouzard et al. (2012).
R-HSA-9686731 (Reactome) Transmembrane protease serine 2 (TMPRSS2), associated with the plasma membrane of the host cell, mediates the hydrolytic cleavage of SARS-CoV-1 Spike (S) protein component of the viral membrane-associate S3:M:E:encapsidated SARS coronavirus genomic RNA: 7a:O-glycosyl 3a tetramer complex associated with ACE2 (Matsuyama et al. 2010; Glowacka et al. 2011; Shulla et al. 2011).
R-HSA-9686790 (Reactome) Inhibition of host cellular functions required for viral replication is considered another host-targeting antiviral strategy. Extensive pharmacological studies have validated ER glucosidases as valuable host antiviral targets against many enveloped viruses (Chang et al. 2013). Most known ER glucosidase inhibitors are imino sugars like 1-deoxynojirimycin (DNJ) and castanopermine (CAST) derivatives (Taylor et al. 1994).

It is generally believed that inhibition of ER glucosidase I and/or II prevents the removal of the terminal glucose moieties on N-linked glycans and results in misfolding and retention of glycoproteins in the ER and ultimate degradation via the ER-associated degradation (ERAD) pathway (Simsek et al. 2005, Alonzi et al. 2013). As a consequence of the abnormal trafficking and degradation of viral glycoproteins, virion assembly and secretion are inhibited (Chang et al. 2009, Taylor et al. 1998).

Long-term suppression of ER glucosidases I and/or II with more potent inhibitors may cause significant side effects, particularly in nerve and immune systems (Sadat et al. 2014).
R-HSA-9687109 (Reactome) It is known that non-structural proteins (nsp) in SARS-CoV viruses induce the formation of ER-bound double membrane vesicles (DMV) in host cells post infection. These DMVs are decorated with microtubule-associated proteins 1A/1B light chain 3B (MAP1LC3B) proteins that are involved in autophagosome formation. However, there is no evidence that DMVs are recruited to the autophagy machinery. Studies show that in some cells sars8b (8b) colocalizes with MAP1LC3B. However, little is known about underlying molecular mechanisms (Shi C S. et al 2019).
R-HSA-9687121 (Reactome) The replicase polyprotein 1a of the human severe acute respiratory syndrome coronavirus (SARS-CoV) is post-translationally cleaved by virally encoded proteases to generate non-structural proteins (nsps). Viral nsps induce the formation of ER-bound double membrane vesicles (DMV) in host cells post infection. These DMVs are decorated with microtubule-associated proteins 1A/1B light chain 3B (MAP1LC3B) proteins that are involved in autophagosome formation. However, there is no evidence that DMVs are recruited to the autophagy machinery. Immunofluorescence studies show that nsp8 colocalizes with MAP1LC3B suggesting a binding event (Prentice E. et al 2004).
R-HSA-9687384 (Reactome) Remdesivir (GS-5734) is an investigational nucleotide analogue drug that was developed for its broad spectrum antiviral potential against Ebola and Marburg virus activity (Siegel et al. 2017). It targets and inhibitis viral RNA-dependent RNA polymerase (nsp12, RdRP), the key component of the replication transcription complex (RTC) (Agostini et al. 2018, Brown et al. 2019, Gordon et al. 2020). Remdesivir is being investigated for potential antiviral activity against SARS-CoV-2 by targeting viral replication (Agostini et al. 2018). Gordon et al. demonstrate remdesivir possesses broad antiviral activity against RNA viruses, including SARS-CoV, MERS-CoV and SARS-CoV-2 in-vitro (Gordon et al. 2020b). It could prevent asymptomatic, mild or moderate COVID-19 cases from progressing to severe disease (clinical trials NCT04252664, NCT04257656) but results so far in infected people have been mixed.

EIDD-2801, is an isopropylester prodrug of the ribonucleoside analogue N4-hydroxycytidine (NHC, EIDD-1931) that shows broad spectrum antiviral activity against various RNA viruses including Ebola, Influenza and CoV (Toots et al. 2019). NHC acts as a competitive alternative substrate for virally encoded RNA-dependent RNA polymerases. NHC was shown to inhibit multiple genetically-distinct Bat-CoV viruses in human primary epithelial cells without affecting cell viability. Prophylactic/therapeutic oral administration of NHC reduced lung titers and prevented acute lung failure in C57B/6 mice infected with CoV. The potency of NHC against multiple coronaviruses, its therapeutic efficacy, and oral bioavailability in vivo, all highlight its potential as an effective antiviral against SARS-CoV-2 and other future zoonotic coronaviruses (Sheahan et al. 2020).
R-HSA-9687388 (Reactome) Remdesivir (GS-5734) is an investigational nucleotide analogue drug that was developed for its broad spectrum antiviral potential against Ebola and Marburg virus activity (Siegel et al. 2017). It targets and inhibitis viral RNA-dependent RNA polymerase (nsp12, RdRP), the key component of the replication transcription complex (RTC) (Agostini et al. 2018, Brown et al. 2019, Gordon et al. 2020). Remdesivir is being investigated for potential antiviral activity against SARS-CoV-2 by targeting viral replication (Agostini et al. 2018). Gordon et al. demonstrate remdesivir possesses broad antiviral activity against RNA viruses, including SARS-CoV, MERS-CoV and SARS-CoV-2 in-vitro (Gordon et al. 2020b). It could prevent asymptomatic, mild or moderate COVID-19 cases from progressing to severe disease (clinical trials NCT04252664, NCT04257656) but results so far in infected people have been mixed.

EIDD-2801, is an isopropylester prodrug of the ribonucleoside analogue N4-hydroxycytidine (NHC, EIDD-1931) that shows broad spectrum antiviral activity against various RNA viruses including Ebola, Influenza and CoV (Toots et al. 2019). NHC acts as a competitive alternative substrate for virally encoded RNA-dependent RNA polymerases. NHC was shown to inhibit multiple genetically-distinct Bat-CoV viruses in human primary epithelial cells without affecting cell viability. Prophylactic/therapeutic oral administration of NHC reduced lung titers and prevented acute lung failure in C57B/6 mice infected with CoV. The potency of NHC against multiple coronaviruses, its therapeutic efficacy, and oral bioavailability in vivo, all highlight its potential as an effective antiviral against SARS-CoV-2 and other future zoonotic coronaviruses (Sheahan et al. 2020).
R-HSA-9687435 (Reactome) The replicase polyprotein 1a of the human severe acute respiratory syndrome coronavirus (SARS-CoV) is post-translationally cleaved by virally encoded proteases to generate non-structural proteins (nsps). Viral nsps induce the formation of ER-bound double membrane vesicles (DMV) in host cells post infection. These DMVs are decorated with microtubule-associated proteins 1A/1B light chain 3B (MAP1LC3B) proteins that are involved in autophagosome formation. However, there is no evidence that DMVs are recruited to the autophagy machinery. Immunofluorescence studies show that nsp6 (Cottam E M. et al 2011) and nsp8 (Prentice E. et al 2004) colocalizes with MAP1LC3B suggesting a binding event. In some cell types, expression of sars9b (9b) triggers the formation of autophagosomes and underlying molecular mechanisms are unclear (Shi C S. et al 2014). Studies also show that sars8b (8b) can trigger cellular stress, which results in a calcineurin dependent Transcription Factor EB (TFEB) activation and its target genes. This leads to an increase in autophagic flux (Shi C S. et al 2019).
R-HSA-9687724 (Reactome) Many GSK-3β inhibitors (GSKi) have been identified. They are known to induce apoptosis in leukemia and pancreatic cancer cells, and can destabilize p53, which may promote cellular death in response to DNA damaging agents (Wang et al, 2008; Beurel et al, 2009). Administration of GSKi inhibited cochlear destruction in cisplatin-injected mice (Park et al, 2009).

Li is a selective ATP competitive inhibitor of GSK-3 (Ryves and Harwood, 2001). Lithium carbonate has been and continously is in clinical trials with bipolar disorder patients (Moore et al, 2009). LY2090314 has been in clinical trials for metastatic pancreatic cancer and acute leukemia ([NCT01632306], [NCT01287520], [NCT01214603]). Clinical trials of GSKi for Alzheimer's disease were unsuccessful.

The use of GSKi remains controversial because of their possibly oncogenic properties. Evaluation of GSKi in clinical trials has been hampered by the fear that inhibition of GSK-3 may stimulate or aid in malignant transformation as GSK-3 can phosphorylate pro-oncogenic factors such as beta-catenin, c-Jun and c-Myc which targets them for degradation (Patel & Woodgett, 2008). However, no studies have been reported suggesting that treatment of mice with GSKi resulted in an increase in cancer incidence. In fact, many patients with bi-polar disorder have been treated with lithium for prolonged periods of time. There does not appear to be any evidence that these patients have increased incidences of cancer (McCubrey et al, 2014).

The GSKi kenpaullone and lithium chloride were found to reduce viral Nucleoprotein phosphorylation in the severe acute respiratory syndrome CoV-infected VeroE6 cells and decrease the viral titer and cytopathic symptoms. Effect of GSK-3 inhibition were reproduced in another coronavirus, the neurotropic JHM strain of mouse hepatitis virus (Wu et al, 2009).
R-HSA-9695415 (Reactome) The CORDITE database contains aggregated information from published and preprint articles about potential drugs, their targets and their interactions (Martin et al. 2020). Different computational approaches reveal drug candidates that may be repurposed for the Covid-19 pandemic. The data provide by this database should be treated as interesting starting points for approved drug candidates that would require clinical testing to determine their efficacy specifically in Covid-19 patients. Here, potential drug candidates for the human ACE2 receptor are described.

Fan et al. constructed a pangolin coronavirus model to screen 2406 approved drugs for their ability to inhibit cytopathic effects and thereby identify candidates for treating Covid-19 infection (Fan et al. 2020). Three drugs, cepharanthine, selamectin and mefloquine hydrochloride, exhibited complete inhibition of cytopathic effects in cell culture. Selamectin is excluded from inclusion here as it is a vetinary drug not approved for human use.

Using Human Pluripotent Stem Cell-derived Colonic Organoids (hPSC-COs) and humanized mouse models, Duan et al. 2020 screened 1280 FDA-approved drugs, which uncovered mycophenolic acid and quinacrine dihydrochloride as promising candidates for SARS-CoV-2 entry inhibition, with greater efficacy than drugs currently being investigated for therapeutic use in COVID-19 (preprint https://www.biorxiv.org/content/10.1101/2020.05.02.073320v1.full).

Molecular dynamic simulations of SARS-CoV-2 spike protein and human ACE2 receptor complexes with stilbenoid analogues potentially having activities against these targets revealed resveratrol to have good affinity for the spike:ACE2 complex. Resveratrol could be a promising anti-COVID-19 drug candidate acting through disruption of the spike protein (Wahedi et al. 2020).

Using a virtual screen of the main targets involved in Covid-19 infection with 7922 FDA-approved drugs, Durdagi et al. 2020 ranked compounds based on their docking scores. Promising ACE2 receptor-binding domain inhibitors included denopamine and rotigaptide amongst the top 5 hits. These compounds could be clinically tested to check whether they may be considered to be use for the treatment of COVID-19 patients (preprint https://chemrxiv.org/articles/preprint/Screening_of_Clinically_Approved_and_Investigation_Drugs_as_Potential_Inhibitors_of_COVID-19_Main_Protease_A_Virtual_Drug_Repurposing_Study/12032712).

Using an in-silico structure-based virtual screening approach, Choudhary et al. 2020 found the FDA-approved drug eptifibatide acetate bound to the virus binding motifs of the ACE2 receptor (preprint https://chemrxiv.org/articles/preprint/Identification_of_SARS-CoV-2_Cell_Entry_Inhibitors_by_Drug_Repurposing_Using_in_Silico_Structure-Based_Virtual_Screening_Approach/12005988).

Redka et al. 2020 utilised a deep learning drug design platform to interrogate the polypharmacological profiles of FDA-approved small molecule drugs or going through clinical trials, with the goal of identifying molecules predicted to modulate targets relevant for COVID-19 treatment. Top drug hits predicted to bind to the ACE2 receptor included a number of broad-spectrum antibiotics such as latamoxef, cefazolin, cefoxitin, enoxacin and pheneticillin, amongst others. This study may identify and prioritise candidates for testing in Covid-19 patients (preprint https://chemrxiv.org/articles/preprint/PolypharmDB_a_Deep_Learning-Based_Resource_Quickly_Identifies_Repurposed_Drug_Candidates_for_COVID-19/12071271).
RB1R-HSA-9682712 (Reactome)
RTC inhibitorsR-HSA-9680262 (Reactome)
RTC inhibitorsR-HSA-9687384 (Reactome)
RTC inhibitorsR-HSA-9687388 (Reactome)
RTCArrowR-HSA-9681840 (Reactome)
RTCArrowR-HSA-9682465 (Reactome)
RTCArrowR-HSA-9686005 (Reactome)
RTCR-HSA-9681314 (Reactome)
RTCR-HSA-9685597 (Reactome)
RTCmim-catalysisR-HSA-9684016 (Reactome)
RTCmim-catalysisR-HSA-9684017 (Reactome)
RTCmim-catalysisR-HSA-9684018 (Reactome)
RTCmim-catalysisR-HSA-9684030 (Reactome)
RTCmim-catalysisR-HSA-9684032 (Reactome)
RTCmim-catalysisR-HSA-9684033 (Reactome)
RTCmim-catalysisR-HSA-9685681 (Reactome)
S-adenosyl-L-homocysteineArrowR-HSA-9684016 (Reactome)
S-adenosyl-L-homocysteineArrowR-HSA-9684017 (Reactome)
S-adenosyl-L-homocysteineArrowR-HSA-9684018 (Reactome)
S-adenosyl-L-homocysteineArrowR-HSA-9684030 (Reactome)
S-adenosyl-L-homocysteineArrowR-HSA-9684032 (Reactome)
S-adenosyl-L-homocysteineArrowR-HSA-9684033 (Reactome)
S-adenosyl-L-methionineR-HSA-9684016 (Reactome)
S-adenosyl-L-methionineR-HSA-9684017 (Reactome)
S-adenosyl-L-methionineR-HSA-9684018 (Reactome)
S-adenosyl-L-methionineR-HSA-9684030 (Reactome)
S-adenosyl-L-methionineR-HSA-9684032 (Reactome)
S-adenosyl-L-methionineR-HSA-9684033 (Reactome)
S1:S2:M:E:

7a:O-glycosyl 3a

tetramer
ArrowR-HSA-9686699 (Reactome)
S1:S2:M:E:encapsidated SARS coronavirus genomic RNA: 7a:O-glycosyl 3a tetramerArrowR-HSA-9686710 (Reactome)
S1:S2:M:E:encapsidated SARS coronavirus genomic RNA: 7a:O-glycosyl 3a tetramerArrowR-HSA-9686731 (Reactome)
S1:S2:M:E:encapsidated SARS coronavirus genomic RNA: 7a:O-glycosyl 3a tetramerR-HSA-9686699 (Reactome)
S3:M:E:encapsidated

SARS coronavirus genomic RNA: 7a:O-glycosyl 3a

tetramer:glycosylated-ACE2
ArrowR-HSA-9678128 (Reactome)
S3:M:E:encapsidated

SARS coronavirus genomic RNA: 7a:O-glycosyl 3a

tetramer:glycosylated-ACE2
ArrowR-HSA-9686711 (Reactome)
S3:M:E:encapsidated

SARS coronavirus genomic RNA: 7a:O-glycosyl 3a

tetramer:glycosylated-ACE2
R-HSA-9686710 (Reactome)
S3:M:E:encapsidated

SARS coronavirus genomic RNA: 7a:O-glycosyl 3a

tetramer:glycosylated-ACE2
R-HSA-9686711 (Reactome)
S3:M:E:encapsidated

SARS coronavirus genomic RNA: 7a:O-glycosyl 3a

tetramer:glycosylated-ACE2
R-HSA-9686731 (Reactome)
S3:M:E:encapsidated

SARS coronavirus genomic RNA:7a:O-glycosyl

3a tetramer
ArrowR-HSA-9685531 (Reactome)
S3:M:E:encapsidated

SARS coronavirus genomic RNA:7a:O-glycosyl

3a tetramer
ArrowR-HSA-9686174 (Reactome)
S3:M:E:encapsidated

SARS coronavirus genomic RNA:7a:O-glycosyl

3a tetramer
R-HSA-9685531 (Reactome)
S3:M:E:encapsidated

SARS coronavirus genomic RNA:7a:O-glycosyl

3a tetramer
R-HSA-9685542 (Reactome)
S3:M:E:encapsidated

SARS coronavirus genomic RNA:O-glycosyl 3a

tetramer
ArrowR-HSA-9684241 (Reactome)
S3:M:E:encapsidated

SARS coronavirus genomic RNA:O-glycosyl 3a

tetramer
R-HSA-9686174 (Reactome)
S3:M:E:encapsidated

SARS coronavirus genomic RNA: 7a:O-glycosyl 3a

tetramer
ArrowR-HSA-9685542 (Reactome)
S3:M:E:encapsidated

SARS coronavirus genomic RNA: 7a:O-glycosyl 3a

tetramer
R-HSA-9678128 (Reactome)
SARS

coronavirus gRNA with secondary

structure:RTC:nascent RNA minus strand
mim-catalysisR-HSA-9682695 (Reactome)
SARS coronavirus

gRNA with secondary

structure:RTC
ArrowR-HSA-9681314 (Reactome)
SARS coronavirus

gRNA with secondary

structure:RTC
R-HSA-9682695 (Reactome)
SARS coronavirus

gRNA:RTC:RNA primer:RTC

inhibitors
ArrowR-HSA-9680262 (Reactome)
SARS coronavirus

gRNA:RTC:RNA primer:RTC

inhibitors
TBarR-HSA-9681674 (Reactome)
SARS coronavirus

gRNA:RTC:RNA primer:RTC

inhibitors
TBarR-HSA-9682563 (Reactome)
SARS coronavirus gRNA:RTC:RNA primerArrowR-HSA-9681651 (Reactome)
SARS coronavirus gRNA:RTC:RNA primerR-HSA-9680262 (Reactome)
SARS coronavirus gRNA:RTC:RNA primerR-HSA-9681674 (Reactome)
SARS coronavirus gRNA:RTC:RNA primermim-catalysisR-HSA-9681674 (Reactome)
SARS coronavirus gRNA:RTC:RNA primermim-catalysisR-HSA-9682563 (Reactome)
SARS coronavirus

gRNA:RTC:nascent RNA minus strand with mismatched

nucleotide
ArrowR-HSA-9682563 (Reactome)
SARS coronavirus

gRNA:RTC:nascent RNA minus strand with mismatched

nucleotide
R-HSA-9682603 (Reactome)
SARS coronavirus

gRNA:RTC:nascent RNA minus strand with mismatched

nucleotide
mim-catalysisR-HSA-9682603 (Reactome)
SARS-CoV-1

gRNA:RTC:nascent RNA minus strand:RTC

inhibitors
ArrowR-HSA-9687388 (Reactome)
SARS-CoV-1

gRNA:RTC:nascent RNA minus strand:RTC

inhibitors
TBarR-HSA-9682465 (Reactome)
SARS-CoV-1

gRNA:RTC:nascent

RNA minus strand
ArrowR-HSA-9681674 (Reactome)
SARS-CoV-1

gRNA:RTC:nascent

RNA minus strand
ArrowR-HSA-9682603 (Reactome)
SARS-CoV-1

gRNA:RTC:nascent

RNA minus strand
R-HSA-9682465 (Reactome)
SARS-CoV-1

gRNA:RTC:nascent

RNA minus strand
R-HSA-9682563 (Reactome)
SARS-CoV-1

gRNA:RTC:nascent

RNA minus strand
R-HSA-9687388 (Reactome)
SARS-CoV-1

gRNA:RTC:nascent

RNA minus strand
mim-catalysisR-HSA-9682465 (Reactome)
SARS-CoV-1 gRNA

complement (minus strand):RTC:RTC

inhibitors
ArrowR-HSA-9687384 (Reactome)
SARS-CoV-1 gRNA

complement (minus strand):RTC:RTC

inhibitors
TBarR-HSA-9681840 (Reactome)
SARS-CoV-1 gRNA

complement (minus

strand):RTC
ArrowR-HSA-9685597 (Reactome)
SARS-CoV-1 gRNA

complement (minus

strand):RTC
R-HSA-9681840 (Reactome)
SARS-CoV-1 gRNA

complement (minus

strand):RTC
R-HSA-9687384 (Reactome)
SARS-CoV-1 gRNA

complement (minus

strand):RTC
mim-catalysisR-HSA-9681840 (Reactome)
SARS-CoV-1 gRNA:RTCArrowR-HSA-9682695 (Reactome)
SARS-CoV-1 gRNA:RTCR-HSA-9681651 (Reactome)
SARS-CoV-1 gRNA:RTCR-HSA-9685639 (Reactome)
SARS-CoV-1 gRNA:RTCmim-catalysisR-HSA-9681651 (Reactome)
SARS-CoV-1 gRNA:RTCmim-catalysisR-HSA-9685639 (Reactome)
SARS-CoV-1 genomic RNA (plus strand)ArrowR-HSA-9681840 (Reactome)
SARS-CoV-1 genomic RNA (plus strand)R-HSA-9682009 (Reactome)
SARS-CoV-1 genomic RNA (plus strand)R-HSA-9684017 (Reactome)
SARS-CoV-1 genomic

RNA complement

(minus strand)
ArrowR-HSA-9682465 (Reactome)
SARS-CoV-1 genomic

RNA complement

(minus strand)
R-HSA-9684018 (Reactome)
SARS-CoV-1 minus

strand subgenomic

mRNAs
ArrowR-HSA-9685639 (Reactome)
SARS-CoV-1 minus

strand subgenomic

mRNAs
R-HSA-9685681 (Reactome)
SARS-CoV-1 plus

strand subgenomic

mRNAs
ArrowR-HSA-9685681 (Reactome)
SARS-CoV-1 plus

strand subgenomic

mRNAs
R-HSA-9684016 (Reactome)
SUMO-p-Ncap

dimer:SARS coronavirus genomic

RNA
ArrowR-HSA-9684229 (Reactome)
SUMO-p-Ncap

dimer:SARS coronavirus genomic

RNA
R-HSA-9684234 (Reactome)
SUMO-p-Ncap dimerArrowR-HSA-9683606 (Reactome)
SUMO-p-Ncap dimerArrowR-HSA-9683630 (Reactome)
SUMO1-K62-ADPr-p-S177-NcapArrowR-HSA-9683687 (Reactome)
SUMO1-K62-ADPr-p-S177-NcapR-HSA-9683634 (Reactome)
SUMO1-K62-p-S177-Ncap dimerArrowR-HSA-9683634 (Reactome)
SUMO1-K62-p-S177-Ncap dimerArrowR-HSA-9683765 (Reactome)
SUMO1-K62-p-S177-Ncap dimerArrowR-HSA-9686709 (Reactome)
SUMO1-K62-p-S177-Ncap dimerR-HSA-9683606 (Reactome)
SUMO1-K62-p-S177-Ncap dimerR-HSA-9683630 (Reactome)
SUMO1-K62-p-S177-Ncap dimerR-HSA-9683765 (Reactome)
SUMO1-K62-p-S177-Ncap dimerR-HSA-9684229 (Reactome)
SUMO1-K62-p-S177-Ncap dimerR-HSA-9684234 (Reactome)
SUMO1:C93-UBE2IR-HSA-9683687 (Reactome)
TMPRSS2 inhibitorsR-HSA-9681514 (Reactome)
TMPRSS2:TMPRSS2 inhibitorsArrowR-HSA-9681514 (Reactome)
TMPRSS2:TMPRSS2 inhibitorsTBarR-HSA-9686731 (Reactome)
TMPRSS2R-HSA-9681514 (Reactome)
TMPRSS2mim-catalysisR-HSA-9686731 (Reactome)
UBE2IArrowR-HSA-9683687 (Reactome)
UDP-GalNAcR-HSA-9683760 (Reactome)
UDP-N-acetyl-alpha-D-glucosamine(2−)R-HSA-9683648 (Reactome)
UDPArrowR-HSA-9683648 (Reactome)
UDPArrowR-HSA-9683760 (Reactome)
UVRAG complexArrowR-HSA-9687435 (Reactome)
Ub-3xPalmC-E pentamerArrowR-HSA-9683635 (Reactome)
Ub-3xPalmC-E pentamerArrowR-HSA-9683670 (Reactome)
Ub-3xPalmC-E pentamerR-HSA-9683635 (Reactome)
Ub-3xPalmC-E pentamerR-HSA-9684238 (Reactome)
Ub-3xPalmC-EArrowR-HSA-9683679 (Reactome)
Ub-3xPalmC-ER-HSA-9683670 (Reactome)
UbR-HSA-9683679 (Reactome)
VCPArrowR-HSA-9686699 (Reactome)
VHLR-HSA-9683455 (Reactome)
ZCRB1:SARS-CoV-1

genomic RNA (plus

strand)
ArrowR-HSA-9682009 (Reactome)
ZCRB1R-HSA-9682009 (Reactome)
a nucleotide sugarR-HSA-9684261 (Reactome)
a nucleotide sugarR-HSA-9684275 (Reactome)
a nucleotide sugarR-HSA-9684290 (Reactome)
beta-D-glucoseArrowR-HSA-9683663 (Reactome)
complex

N-glycan-PALM-Spike

trimer
ArrowR-HSA-9683648 (Reactome)
complex

N-glycan-PALM-Spike

trimer
R-HSA-9684241 (Reactome)
encapsidated SARS

coronavirus genomic

RNA (plus strand)
ArrowR-HSA-9686699 (Reactome)
encapsidated SARS

coronavirus genomic

RNA (plus strand)
R-HSA-9686709 (Reactome)
encapsidated SARS

coronavirus genomic

RNA
ArrowR-HSA-9684234 (Reactome)
encapsidated SARS

coronavirus genomic

RNA
R-HSA-9684238 (Reactome)
glycosylated-ACE2:ACE2 inhibitorsArrowR-HSA-9695415 (Reactome)
glycosylated-ACE2ArrowR-HSA-9686710 (Reactome)
glycosylated-ACE2R-HSA-9678128 (Reactome)
glycosylated-ACE2R-HSA-9695415 (Reactome)
m7G(5')pppAm-SARS-CoV-1 plus strand subgenomic mRNAsArrowR-HSA-9684033 (Reactome)
m7G(5')pppAm-SARS-CoV-1 plus strand subgenomic mRNAsR-HSA-9685906 (Reactome)
m7G(5')pppAm-capped

SARS-CoV-1 genomic

RNA (plus strand)
ArrowR-HSA-9684032 (Reactome)
m7G(5')pppAm-capped

SARS-CoV-1 genomic

RNA (plus strand)
R-HSA-9685519 (Reactome)
m7G(5')pppAm-capped

SARS-CoV-1 genomic RNA complement

(minus strand)
ArrowR-HSA-9681840 (Reactome)
m7G(5')pppAm-capped

SARS-CoV-1 genomic RNA complement

(minus strand)
ArrowR-HSA-9684030 (Reactome)
m7G(5')pppAm-capped

SARS-CoV-1 genomic RNA complement

(minus strand)
R-HSA-9685597 (Reactome)
m7G(5')pppAm-capped,

polyadenylated SARS-CoV-1 subgenomic mRNAs

(plus strand)
ArrowR-HSA-9685906 (Reactome)
m7G(5')pppAm-capped,

polyadenylated SARS-CoV-1 genomic

RNA (plus strand)
ArrowR-HSA-9682465 (Reactome)
m7G(5')pppAm-capped,

polyadenylated SARS-CoV-1 genomic

RNA (plus strand)
ArrowR-HSA-9685519 (Reactome)
m7G(5')pppAm-capped,

polyadenylated SARS-CoV-1 genomic

RNA (plus strand)
R-HSA-9684229 (Reactome)
m7G(5')pppAm-capped,

polyadenylated SARS-CoV-1 genomic

RNA (plus strand)
R-HSA-9684277 (Reactome)
m7G(5')pppAm-capped,

polyadenylated SARS-CoV-1 genomic

RNA (plus strand)
R-HSA-9684301 (Reactome)
m7G(5')pppAm-capped,polyadenylated mRNA2R-HSA-9683624 (Reactome)
m7G(5')pppAm-capped,polyadenylated mRNA3R-HSA-9683618 (Reactome)
m7G(5')pppAm-capped,polyadenylated mRNA4R-HSA-9683656 (Reactome)
m7G(5')pppAm-capped,polyadenylated mRNA5R-HSA-9683622 (Reactome)
m7G(5')pppAm-capped,polyadenylated-mRNA9R-HSA-9683735 (Reactome)
m7GpppA-SARS-CoV-1

plus strand

subgenomic mRNAs
R-HSA-9684033 (Reactome)
m7GpppA-capped

SARS-CoV-1 genomic

RNA (plus strand)
ArrowR-HSA-9684017 (Reactome)
m7GpppA-capped

SARS-CoV-1 genomic

RNA (plus strand)
ArrowR-HSA-9686709 (Reactome)
m7GpppA-capped

SARS-CoV-1 genomic

RNA (plus strand)
R-HSA-9681314 (Reactome)
m7GpppA-capped

SARS-CoV-1 genomic

RNA (plus strand)
R-HSA-9684032 (Reactome)
m7GpppA-capped

SARS-CoV-1 genomic RNA complement

(minus strand)
ArrowR-HSA-9684018 (Reactome)
m7GpppA-capped

SARS-CoV-1 genomic RNA complement

(minus strand)
R-HSA-9684030 (Reactome)
nascent EArrowR-HSA-9683656 (Reactome)
nascent ER-HSA-9683669 (Reactome)
nascent ER-HSA-9683720 (Reactome)
nascent MArrowR-HSA-9683622 (Reactome)
nascent MR-HSA-9683718 (Reactome)
nascent MR-HSA-9683751 (Reactome)
nascent SpikeArrowR-HSA-9683624 (Reactome)
nascent SpikeR-HSA-9683755 (Reactome)
nsp1-4R-HSA-9684321 (Reactome)
nsp1-4R-HSA-9684336 (Reactome)
nsp10:nsp14ArrowR-HSA-9682544 (Reactome)
nsp10:nsp14R-HSA-9682258 (Reactome)
nsp10R-HSA-9682544 (Reactome)
nsp10R-HSA-9683429 (Reactome)
nsp13:DDX5ArrowR-HSA-9682631 (Reactome)
nsp15 hexamerArrowR-HSA-9682718 (Reactome)
nsp15 hexamerR-HSA-9682712 (Reactome)
nsp15 hexamerR-HSA-9683393 (Reactome)
nsp15:RB1ArrowR-HSA-9682712 (Reactome)
nsp16:VHLArrowR-HSA-9683455 (Reactome)
nsp16:nsp10ArrowR-HSA-9683429 (Reactome)
nsp16:nsp10R-HSA-9686005 (Reactome)
nsp1ArrowR-HSA-9684321 (Reactome)
nsp1ArrowR-HSA-9684336 (Reactome)
nsp2ArrowR-HSA-9684321 (Reactome)
nsp2ArrowR-HSA-9684336 (Reactome)
nsp3-4ArrowR-HSA-9684336 (Reactome)
nsp3-4R-HSA-9684275 (Reactome)
nsp3-4R-HSA-9684352 (Reactome)
nsp3:nsp4:nsp6ArrowR-HSA-9686013 (Reactome)
nsp3:nsp4:nsp6R-HSA-9686005 (Reactome)
nsp3:nsp4ArrowR-HSA-9686015 (Reactome)
nsp3:nsp4R-HSA-9686013 (Reactome)
nsp3ArrowR-HSA-9684321 (Reactome)
nsp3ArrowR-HSA-9684352 (Reactome)
nsp3R-HSA-9684290 (Reactome)
nsp4ArrowR-HSA-9684321 (Reactome)
nsp4ArrowR-HSA-9684352 (Reactome)
nsp4R-HSA-9684261 (Reactome)
nsp5R-HSA-9684323 (Reactome)
nsp6ArrowR-HSA-9686015 (Reactome)
nsp6R-HSA-9686013 (Reactome)
nsp6R-HSA-9686015 (Reactome)
nsp7:nsp8:nsp12:nsp14:nsp10:nsp13:nsp15ArrowR-HSA-9683393 (Reactome)
nsp7:nsp8:nsp12:nsp14:nsp10:nsp13:nsp15R-HSA-9686005 (Reactome)
nsp7:nsp8:nsp12:nsp14:nsp10:nsp13ArrowR-HSA-9682626 (Reactome)
nsp7:nsp8:nsp12:nsp14:nsp10:nsp13R-HSA-9683393 (Reactome)
nsp7:nsp8:nsp12:nsp14:nsp10ArrowR-HSA-9682258 (Reactome)
nsp7:nsp8:nsp12:nsp14:nsp10R-HSA-9682626 (Reactome)
nsp7:nsp8:nsp12ArrowR-HSA-9680811 (Reactome)
nsp7:nsp8:nsp12R-HSA-9682258 (Reactome)
nsp7:nsp8ArrowR-HSA-9680812 (Reactome)
nsp7:nsp8R-HSA-9680811 (Reactome)
nsp7R-HSA-9680812 (Reactome)
nsp8:MAP1LC3BArrowR-HSA-9687121 (Reactome)
nsp8R-HSA-9680811 (Reactome)
nsp8R-HSA-9680812 (Reactome)
nsp8R-HSA-9687121 (Reactome)
nsp9 dimerArrowR-HSA-9684282 (Reactome)
nsp9R-HSA-9684282 (Reactome)
nucleoside 5'-diphosphate(3-)ArrowR-HSA-9684261 (Reactome)
nucleoside 5'-diphosphate(3-)ArrowR-HSA-9684275 (Reactome)
nucleoside 5'-diphosphate(3-)ArrowR-HSA-9684290 (Reactome)
nucleoside 5'-diphosphate(3−)ArrowR-HSA-9683669 (Reactome)
nucleoside 5'-diphosphate(3−)ArrowR-HSA-9683751 (Reactome)
nucleoside 5'-diphosphate(3−)ArrowR-HSA-9683755 (Reactome)
nucleotide-sugarR-HSA-9683669 (Reactome)
nucleotide-sugarR-HSA-9683751 (Reactome)
nucleotide-sugarR-HSA-9683755 (Reactome)
p-S177,S181,S185,S187,S189,S191,S195,T199,S203,S207-NArrowR-HSA-9681627 (Reactome)
p-S177-NcapArrowR-HSA-9683664 (Reactome)
p-S177-NcapR-HSA-9686061 (Reactome)
palmitoyl-CoAR-HSA-9683653 (Reactome)
palmitoyl-CoAR-HSA-9683720 (Reactome)
pp1a dimerArrowR-HSA-9684350 (Reactome)
pp1a dimermim-catalysisR-HSA-9684351 (Reactome)
pp1a-nsp1-4ArrowR-HSA-9684273 (Reactome)
pp1a-nsp1-4ArrowR-HSA-9684351 (Reactome)
pp1a-nsp1-4mim-catalysisR-HSA-9684336 (Reactome)
pp1a-nsp10ArrowR-HSA-9684309 (Reactome)
pp1a-nsp11ArrowR-HSA-9684309 (Reactome)
pp1a-nsp5ArrowR-HSA-9684273 (Reactome)
pp1a-nsp5ArrowR-HSA-9684351 (Reactome)
pp1a-nsp6-11ArrowR-HSA-9684273 (Reactome)
pp1a-nsp6-11ArrowR-HSA-9684351 (Reactome)
pp1a-nsp6-11R-HSA-9684309 (Reactome)
pp1a-nsp6ArrowR-HSA-9684309 (Reactome)
pp1a-nsp7ArrowR-HSA-9684309 (Reactome)
pp1a-nsp8ArrowR-HSA-9684309 (Reactome)
pp1a-nsp9ArrowR-HSA-9684309 (Reactome)
pp1aArrowR-HSA-9684301 (Reactome)
pp1aR-HSA-9684273 (Reactome)
pp1aR-HSA-9684350 (Reactome)
pp1aR-HSA-9684351 (Reactome)
pp1ab-nsp1-4ArrowR-HSA-9684340 (Reactome)
pp1ab-nsp10ArrowR-HSA-9684340 (Reactome)
pp1ab-nsp12ArrowR-HSA-9684340 (Reactome)
pp1ab-nsp12R-HSA-9680811 (Reactome)
pp1ab-nsp13ArrowR-HSA-9684340 (Reactome)
pp1ab-nsp13R-HSA-9682626 (Reactome)
pp1ab-nsp13R-HSA-9682631 (Reactome)
pp1ab-nsp14ArrowR-HSA-9684340 (Reactome)
pp1ab-nsp14R-HSA-9682544 (Reactome)
pp1ab-nsp15ArrowR-HSA-9684340 (Reactome)
pp1ab-nsp15R-HSA-9682718 (Reactome)
pp1ab-nsp16ArrowR-HSA-9684340 (Reactome)
pp1ab-nsp16R-HSA-9683429 (Reactome)
pp1ab-nsp16R-HSA-9683455 (Reactome)
pp1ab-nsp5ArrowR-HSA-9684340 (Reactome)
pp1ab-nsp6ArrowR-HSA-9684340 (Reactome)
pp1ab-nsp7ArrowR-HSA-9684340 (Reactome)
pp1ab-nsp8ArrowR-HSA-9684340 (Reactome)
pp1ab-nsp9ArrowR-HSA-9684340 (Reactome)
pp1abArrowR-HSA-9684277 (Reactome)
pp1abR-HSA-9684340 (Reactome)
sialyltransferasesmim-catalysisR-HSA-9683769 (Reactome)
trimmed

N-glycan-PALM-Spike

trimer
ArrowR-HSA-9683719 (Reactome)
trimmed

N-glycan-PALM-Spike

trimer
ArrowR-HSA-9683764 (Reactome)
trimmed

N-glycan-PALM-Spike

trimer
R-HSA-9683648 (Reactome)
trimmed

N-glycan-PALM-Spike

trimer
R-HSA-9683764 (Reactome)
trimmed N-glycan-PALM-SpikeArrowR-HSA-9683653 (Reactome)
trimmed N-glycan-PALM-SpikeR-HSA-9683719 (Reactome)
trimmed N-glycan SpikeArrowR-HSA-9683772 (Reactome)
trimmed N-glycan SpikeR-HSA-9683653 (Reactome)
trimmed unfolded N-glycan SpikeArrowR-HSA-9683663 (Reactome)
trimmed unfolded N-glycan SpikeR-HSA-9683772 (Reactome)
α-KetoamidesR-HSA-9681596 (Reactome)
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