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(-)Asym./Biol. Unit
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Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF SARS-COV MAIN PROTEASE H41A MUTANT IN COMPLEX WITH AN N-TERMINAL SUBSTRATE
 
Authors :  X. Y. Xue, H. T. Yang, F. Xue, M. Bartlam, Z. H. Rao
Date :  05 Jun 07  (Deposition) - 12 Feb 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Coronavirus; Sars-Cov; Main Protease; 3C-Like Proteinase; Substrate, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  X. Xue, H. Yu, H. Yang, F. Xue, Z. Wu, W. Shen, J. Li, Z. Zhou, Y. Ding, Q. Zhao, X. C. Zhang, M. Liao, M. Bartlam, Z. Rao
Structures Of Two Coronavirus Main Proteases: Implications For Substrate Binding And Antiviral Drug Design.
J. Virol. V. 82 2515 2008
PubMed-ID: 18094151  |  Reference-DOI: 10.1128/JVI.02114-07

(-) Compounds

Molecule 1 - SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS (SARS-COV)
    ChainsA, B
    EC Number3.4.22.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPGEX-6P-1
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    GeneREP
    MutationYES
    Organism ScientificSARS CORONAVIRUS
    Organism Taxid228407
    StrainBJ01
 
Molecule 2 - POLYPEPTIDE CHAIN
    ChainsC, D
    EngineeredYES
    Other DetailsCHEMICALLY SYNTHESIZED.
    SyntheticYES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2Q6G)

(-) Sites  (0, 0)

(no "Site" information available for 2Q6G)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Q6G)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2Q6G)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (4, 8)

Asymmetric/Biological Unit (4, 8)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_R1AB_CVHSA_047 *Q3429PR1AB_CVHSA  ---  ---A/BQ189P
2UniProtVAR_R1A_CVHSA_047 *Q3429PR1A_CVHSA  ---  ---A/BQ189P
3UniProtVAR_R1AB_CVHSA_048 *D3488ER1AB_CVHSA  ---  ---A/BD248E
4UniProtVAR_R1A_CVHSA_048 *D3488ER1A_CVHSA  ---  ---A/BD248E
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1M_PROPS51442 Coronavirus main protease (M-pro) domain profile.R1A_CVHSA3241-3546
 
  2A:1-305
B:1-302
R1AB_CVHSA3241-3546
 
  2A:1-305
B:1-302

(-) Exons   (0, 0)

(no "Exon" information available for 2Q6G)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:305
 aligned with R1AB_CVHSA | P0C6X7 from UniProtKB/Swiss-Prot  Length:7073

    Alignment length:305
                                  3250      3260      3270      3280      3290      3300      3310      3320      3330      3340      3350      3360      3370      3380      3390      3400      3410      3420      3430      3440      3450      3460      3470      3480      3490      3500      3510      3520      3530      3540     
          R1AB_CVHSA   3241 SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDTVYCPRHVICTAEDMLNPNYEDLLIRKSNHSFLVQAGNVQLRVIGHSMQNCLLRLKVDTSNPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNHTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGKFYGPFVDRQTAQAAGTDTTITLNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCAALKELLQNGMNGRTILGSTILEDEFTPFDVVRQCSGVTF 3545
               SCOP domains d2q6ga_ A: Coronavirus main proteinase (3Cl-pro, putative coronavirus nsp2)                                                                                                                                                                                                                                       SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhh.eeeeee..eeeeeeee..eeeee.hhhh........hhhhhhhh.hhhhheeee..eee.eeeeeee..eeeeee.........eee.......eeeeeeee..eeeeeeeee..................eeeeee..eeeeeeeeeee.....eeee........................hhhhhhhhhhhhhhh...........hhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.................hhhhhhhhhh.... Sec.struct. author
             SAPs(SNPs) (1) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------P----------------------------------------------------------E--------------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------P----------------------------------------------------------E--------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE M_PRO  PDB: A:1-305 UniProt: 3241-3546                                                                                                                                                                                                                                                                            PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2q6g A    1 SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDTVYCPRAVICTAEDMLNPNYEDLLIRKSNHSFLVQAGNVQLRVIGHSMQNCLLRLKVDTSNPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNHTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGKFYGPFVDRQTAQAAGTDTTITLNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCAALKELLQNGMNGRTILGSTILEDEFTPFDVVRQCSGVTF  305
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300     

Chain A from PDB  Type:PROTEIN  Length:305
 aligned with R1A_CVHSA | P0C6U8 from UniProtKB/Swiss-Prot  Length:4382

    Alignment length:305
                                  3250      3260      3270      3280      3290      3300      3310      3320      3330      3340      3350      3360      3370      3380      3390      3400      3410      3420      3430      3440      3450      3460      3470      3480      3490      3500      3510      3520      3530      3540     
           R1A_CVHSA   3241 SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDTVYCPRHVICTAEDMLNPNYEDLLIRKSNHSFLVQAGNVQLRVIGHSMQNCLLRLKVDTSNPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNHTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGKFYGPFVDRQTAQAAGTDTTITLNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCAALKELLQNGMNGRTILGSTILEDEFTPFDVVRQCSGVTF 3545
               SCOP domains d2q6ga_ A: Coronavirus main proteinase (3Cl-pro, putative coronavirus nsp2)                                                                                                                                                                                                                                       SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhh.eeeeee..eeeeeeee..eeeee.hhhh........hhhhhhhh.hhhhheeee..eee.eeeeeee..eeeeee.........eee.......eeeeeeee..eeeeeeeee..................eeeeee..eeeeeeeeeee.....eeee........................hhhhhhhhhhhhhhh...........hhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.................hhhhhhhhhh.... Sec.struct. author
             SAPs(SNPs) (1) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------P----------------------------------------------------------E--------------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------P----------------------------------------------------------E--------------------------------------------------------- SAPs(SNPs) (2)
                PROSITE (2) M_PRO  PDB: A:1-305 UniProt: 3241-3546                                                                                                                                                                                                                                                                            PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2q6g A    1 SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDTVYCPRAVICTAEDMLNPNYEDLLIRKSNHSFLVQAGNVQLRVIGHSMQNCLLRLKVDTSNPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNHTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGKFYGPFVDRQTAQAAGTDTTITLNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCAALKELLQNGMNGRTILGSTILEDEFTPFDVVRQCSGVTF  305
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300     

Chain B from PDB  Type:PROTEIN  Length:302
 aligned with R1AB_CVHSA | P0C6X7 from UniProtKB/Swiss-Prot  Length:7073

    Alignment length:302
                                  3250      3260      3270      3280      3290      3300      3310      3320      3330      3340      3350      3360      3370      3380      3390      3400      3410      3420      3430      3440      3450      3460      3470      3480      3490      3500      3510      3520      3530      3540  
          R1AB_CVHSA   3241 SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDTVYCPRHVICTAEDMLNPNYEDLLIRKSNHSFLVQAGNVQLRVIGHSMQNCLLRLKVDTSNPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNHTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGKFYGPFVDRQTAQAAGTDTTITLNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCAALKELLQNGMNGRTILGSTILEDEFTPFDVVRQCSG 3542
               SCOP domains d2q6gb_ B: Coronavirus main proteinase (3Cl-pro, putative coronavirus nsp2)                                                                                                                                                                                                                                    SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------------------Peptidase_C30-2q6gB01 B:29-302                                                                                                                                                                                                                                                     Pfam domains (1)
           Pfam domains (2) ----------------------------Peptidase_C30-2q6gB02 B:29-302                                                                                                                                                                                                                                                     Pfam domains (2)
         Sec.struct. author .........hhhhhh.eeeeee..eeeeeeee..eeeee.hhhh.hhhhhh.hhhhhhhh.hhhhheeee..eee.eeeeeee..eeeeee........eeee.......eeeeeeee..eeeeeeeee..................eeeeee..eeeeeeeeeee.....eeee........................hhhhhhhhhhhhhhh...........hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhh Sec.struct. author
             SAPs(SNPs) (1) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------P----------------------------------------------------------E------------------------------------------------------ SAPs(SNPs) (1)
             SAPs(SNPs) (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------P----------------------------------------------------------E------------------------------------------------------ SAPs(SNPs) (2)
                    PROSITE M_PRO  PDB: B:1-302 UniProt: 3241-3546                                                                                                                                                                                                                                                                         PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2q6g B    1 SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDTVYCPRAVICTAEDMLNPNYEDLLIRKSNHSFLVQAGNVQLRVIGHSMQNCLLRLKVDTSNPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNHTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGKFYGPFVDRQTAQAAGTDTTITLNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCAALKELLQNGMNGRTILGSTILEDEFTPFDVVRQCSG  302
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300  

Chain B from PDB  Type:PROTEIN  Length:302
 aligned with R1A_CVHSA | P0C6U8 from UniProtKB/Swiss-Prot  Length:4382

    Alignment length:302
                                  3250      3260      3270      3280      3290      3300      3310      3320      3330      3340      3350      3360      3370      3380      3390      3400      3410      3420      3430      3440      3450      3460      3470      3480      3490      3500      3510      3520      3530      3540  
           R1A_CVHSA   3241 SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDTVYCPRHVICTAEDMLNPNYEDLLIRKSNHSFLVQAGNVQLRVIGHSMQNCLLRLKVDTSNPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNHTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGKFYGPFVDRQTAQAAGTDTTITLNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCAALKELLQNGMNGRTILGSTILEDEFTPFDVVRQCSG 3542
               SCOP domains d2q6gb_ B: Coronavirus main proteinase (3Cl-pro, putative coronavirus nsp2)                                                                                                                                                                                                                                    SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------------------Peptidase_C30-2q6gB01 B:29-302                                                                                                                                                                                                                                                     Pfam domains (1)
           Pfam domains (2) ----------------------------Peptidase_C30-2q6gB02 B:29-302                                                                                                                                                                                                                                                     Pfam domains (2)
         Sec.struct. author .........hhhhhh.eeeeee..eeeeeeee..eeeee.hhhh.hhhhhh.hhhhhhhh.hhhhheeee..eee.eeeeeee..eeeeee........eeee.......eeeeeeee..eeeeeeeee..................eeeeee..eeeeeeeeeee.....eeee........................hhhhhhhhhhhhhhh...........hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhh Sec.struct. author
             SAPs(SNPs) (1) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------P----------------------------------------------------------E------------------------------------------------------ SAPs(SNPs) (1)
             SAPs(SNPs) (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------P----------------------------------------------------------E------------------------------------------------------ SAPs(SNPs) (2)
                PROSITE (2) M_PRO  PDB: B:1-302 UniProt: 3241-3546                                                                                                                                                                                                                                                                         PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2q6g B    1 SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDTVYCPRAVICTAEDMLNPNYEDLLIRKSNHSFLVQAGNVQLRVIGHSMQNCLLRLKVDTSNPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNHTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGKFYGPFVDRQTAQAAGTDTTITLNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCAALKELLQNGMNGRTILGSTILEDEFTPFDVVRQCSG  302
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300  

Chain C from PDB  Type:PROTEIN  Length:11
                                            
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author ...ee..ee.. Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                2q6g C    1 TSAVLQSGFRK   11
                                    10 

Chain D from PDB  Type:PROTEIN  Length:8
                                         
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ........ Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                2q6g D    1 TSAVLQSG    8

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Q6G)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (65, 100)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (R1AB_CVHSA | P0C6X7)
molecular function
    GO:0000175    3'-5'-exoribonuclease activity    Catalysis of the sequential cleavage of mononucleotides from a free 3' terminus of an RNA molecule.
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:1990380    Lys48-specific deubiquitinase activity    Hydrolysis of Lys48-linked ubiquitin unit(s) from a ubiquitinated protein.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003968    RNA-directed 5'-3' RNA polymerase activity    Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1); uses an RNA template, i.e. the catalysis of RNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time.
    GO:0004197    cysteine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
    GO:0008234    cysteine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
    GO:0003725    double-stranded RNA binding    Interacting selectively and non-covalently with double-stranded RNA.
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    GO:0004527    exonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end.
    GO:0016896    exoribonuclease activity, producing 5'-phosphomonoesters    Catalysis of the hydrolysis of ester linkages within ribonucleic acids by removing nucleotide residues from the 3' or 5' end to yield 5' phosphomonoesters.
    GO:0004386    helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016817    hydrolase activity, acting on acid anhydrides    Catalysis of the hydrolysis of any acid anhydride.
    GO:0016788    hydrolase activity, acting on ester bonds    Catalysis of the hydrolysis of any ester bond.
    GO:0004482    mRNA (guanine-N7-)-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + G(5')pppR-RNA = S-adenosyl-L-homocysteine + m7G(5')pppR-RNA. m7G(5')pppR-RNA is mRNA containing an N7-methylguanine cap; R may be guanosine or adenosine.
    GO:0004483    mRNA (nucleoside-2'-O-)-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + m7G(5')pppR-RNA = S-adenosyl-L-homocysteine + m7G(5')pppRm-RNA. R may be guanosine or adenosine.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    GO:0008242    omega peptidase activity    Catalysis of the removal of terminal peptide residues that are substituted, cyclized or linked by isopeptide bonds (peptide linkages other than those of alpha-carboxyl to alpha-amino groups).
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0003727    single-stranded RNA binding    Interacting selectively and non-covalently with single-stranded RNA.
    GO:0036459    thiol-dependent ubiquitinyl hydrolase activity    Catalysis of the thiol-dependent hydrolysis of an ester, thioester, amide, peptide or isopeptide bond formed by the C-terminal glycine of ubiquitin.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006370    7-methylguanosine mRNA capping    Addition of the 7-methylguanosine cap to the 5' end of a nascent messenger RNA transcript.
    GO:0036265    RNA (guanine-N7)-methylation    The addition of a methyl group to the N7 atom in the base portion of a guanine nucleotide residue in an RNA molecule.
    GO:0090503    RNA phosphodiester bond hydrolysis, exonucleolytic    The chemical reactions and pathways involving the hydrolysis of terminal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
    GO:0030683    evasion or tolerance by virus of host immune response    Any process, either active or passive, by which a virus avoids the effects of the host organism's immune response. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0039595    induction by virus of catabolism of host mRNA    The process in which a virus increases the frequency, rate or extent of the breakdown of host messenger RNA (mRNA).
    GO:0039520    induction by virus of host autophagy    Any process in which a virus activates or increases the frequency, rate or extent of autophagy in the host.
    GO:0080009    mRNA methylation    The posttranscriptional addition of methyl groups to specific residues in an mRNA molecule.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0039519    modulation by virus of host autophagy    Any process in which a virus effect a change in the frequency, rate or extent of autophagy in the host.
    GO:0039648    modulation by virus of host protein ubiquitination    Any process in which a virus modulates the frequency, rate or extent of protein ubiquitination in the host organism. Ubiquitination is the process in which one or more ubiquitin groups are added to a protein.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:2000158    positive regulation of ubiquitin-specific protease activity    Any process that activates or increases the frequency, rate or extent of ubiquitin-specific protease (deubiquitinase) activity.
    GO:0039690    positive stranded viral RNA replication    A viral genome replication process where the template genome is positive stranded, single stranded RNA ((+)ssRNA). Replication of the positive strand leads to dsRNA formation, which in turn is transcribed into positive single stranded RNA.
    GO:0071108    protein K48-linked deubiquitination    A protein deubiquitination process in which a K48-linked ubiquitin chain, i.e. a polymer of ubiquitin formed by linkages between lysine residues at position 48 of the ubiquitin monomers, is removed from a protein.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0039549    suppression by virus of host IRF3 activity by inhibition of IRF3 phosphorylation    Any process in which a virus stops, prevents, or reduces the rate or extent of the phosphorylation of IRF3 (interferon regulatory factor-3), thereby inhibiting IRF3 activation. In response to signaling from RIG-1/MDA-5 receptors, IRF3 is phosphorylated on multiple serine and threonine residues; phosphorylation results in the cytoplasm-to-nucleus translocation of IRF3, DNA binding, and increased transcriptional activation of interferon-encoding genes.
    GO:0039579    suppression by virus of host ISG15 activity    Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of host ubiquitin-like protein ISG15 activity. ISG15 is a ubiquitin-like protein that is conjugated to lysine residues on various target proteins. Viruses escape from the antiviral activity of ISG15 by using different mechanisms; the influenza B virus NS1 protein for instance blocks the covalent linkage of ISG15 to its target proteins by directly interacting with ISG15. The papain-like protease from the coronavirus cleaves ISG15 derivatives.
    GO:0039644    suppression by virus of host NF-kappaB transcription factor activity    Any process in which a virus stops, prevents, or reduces the activity of host NF-kappaB activity.
    GO:0039657    suppression by virus of host gene expression    Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of gene expression in the host organism. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form.
    GO:0039503    suppression by virus of host innate immune response    Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of the innate immune response of the host organism, the host's first line of defense.
    GO:0039604    suppression by virus of host translation    Any process in which a virus prevents or reduces the frequency, rate or extent of translation of host mRNA.
    GO:0039502    suppression by virus of host type I interferon-mediated signaling pathway    Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of type I interferon-mediated signaling in the host organism. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
    GO:0001172    transcription, RNA-templated    The cellular synthesis of RNA on a template of RNA.
    GO:0039694    viral RNA genome replication    The replication of a viral RNA genome.
    GO:0019079    viral genome replication    Any process involved directly in viral genome replication, including viral nucleotide metabolism.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
    GO:0019082    viral protein processing    Any protein maturation process achieved by the cleavage of a peptide bond or bonds within a viral protein.
    GO:0019083    viral transcription    The process by which a viral genome, or part of a viral genome, is transcribed within the host cell.
cellular component
    GO:0030430    host cell cytoplasm    The cytoplasm of a host cell.
    GO:0044172    host cell endoplasmic reticulum-Golgi intermediate compartment    A complex system of membrane-bounded compartments located between host cell endoplasmic reticulum (ER) and the host Golgi complex, with a distinctive membrane protein composition; involved in ER-to-Golgi transport.
    GO:0033644    host cell membrane    Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0044220    host cell perinuclear region of cytoplasm    The host cell cytoplasm situated near, or occurring around, the host nucleus.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Chain A,B   (R1A_CVHSA | P0C6U8)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003968    RNA-directed 5'-3' RNA polymerase activity    Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1); uses an RNA template, i.e. the catalysis of RNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time.
    GO:0004197    cysteine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
    GO:0008234    cysteine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016817    hydrolase activity, acting on acid anhydrides    Catalysis of the hydrolysis of any acid anhydride.
    GO:0016788    hydrolase activity, acting on ester bonds    Catalysis of the hydrolysis of any ester bond.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0008242    omega peptidase activity    Catalysis of the removal of terminal peptide residues that are substituted, cyclized or linked by isopeptide bonds (peptide linkages other than those of alpha-carboxyl to alpha-amino groups).
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0036459    thiol-dependent ubiquitinyl hydrolase activity    Catalysis of the thiol-dependent hydrolysis of an ester, thioester, amide, peptide or isopeptide bond formed by the C-terminal glycine of ubiquitin.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0030683    evasion or tolerance by virus of host immune response    Any process, either active or passive, by which a virus avoids the effects of the host organism's immune response. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0039595    induction by virus of catabolism of host mRNA    The process in which a virus increases the frequency, rate or extent of the breakdown of host messenger RNA (mRNA).
    GO:0039520    induction by virus of host autophagy    Any process in which a virus activates or increases the frequency, rate or extent of autophagy in the host.
    GO:0039648    modulation by virus of host protein ubiquitination    Any process in which a virus modulates the frequency, rate or extent of protein ubiquitination in the host organism. Ubiquitination is the process in which one or more ubiquitin groups are added to a protein.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0039548    suppression by virus of host IRF3 activity    Any process in which a virus stops, prevents, or reduces the activity of host IRF3 (interferon regulatory factor-3), a transcription factor in the RIG-I/MDA-5 signaling pathway. Viral infection triggers phosphorylation of cytoplasmic IRF3, which allows IRF3 to form a homodimer, migrate to the nucleus, and activate transcription of IFN-alpha and IFN-beta genes.
    GO:0039579    suppression by virus of host ISG15 activity    Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of host ubiquitin-like protein ISG15 activity. ISG15 is a ubiquitin-like protein that is conjugated to lysine residues on various target proteins. Viruses escape from the antiviral activity of ISG15 by using different mechanisms; the influenza B virus NS1 protein for instance blocks the covalent linkage of ISG15 to its target proteins by directly interacting with ISG15. The papain-like protease from the coronavirus cleaves ISG15 derivatives.
    GO:0039657    suppression by virus of host gene expression    Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of gene expression in the host organism. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form.
    GO:0039503    suppression by virus of host innate immune response    Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of the innate immune response of the host organism, the host's first line of defense.
    GO:0039502    suppression by virus of host type I interferon-mediated signaling pathway    Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of type I interferon-mediated signaling in the host organism. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
    GO:0001172    transcription, RNA-templated    The cellular synthesis of RNA on a template of RNA.
    GO:0019079    viral genome replication    Any process involved directly in viral genome replication, including viral nucleotide metabolism.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
    GO:0019082    viral protein processing    Any protein maturation process achieved by the cleavage of a peptide bond or bonds within a viral protein.
cellular component
    GO:0030430    host cell cytoplasm    The cytoplasm of a host cell.
    GO:0033644    host cell membrane    Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0044220    host cell perinuclear region of cytoplasm    The host cell cytoplasm situated near, or occurring around, the host nucleus.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        R1AB_CVHSA | P0C6X71o5s 1p76 1p9t 1pa5 1puk 1q1x 1q2w 1qz8 1sxf 1uj1 1uk2 1uk3 1uk4 1uw7 1wof 1ysy 1z1i 1z1j 2a5a 2a5i 2a5k 2acf 2ahm 2aj5 2alv 2amd 2amq 2bx3 2bx4 2c3s 2d2d 2duc 2fav 2fe8 2fyg 2g1f 2g9t 2ga6 2gdt 2gri 2gt7 2gt8 2gtb 2gx4 2gz7 2gz8 2gz9 2h2z 2h85 2hob 2hsx 2idy 2jzd 2jze 2jzf 2k87 2op9 2ozk 2pwx 2qc2 2qcy 2qiq 2rhb 2rnk 2v6n 2vj1 2xyq 2xyr 2xyv 2z3c 2z3d 2z3e 2z94 2z9g 2z9j 2z9k 2z9l 3d62 3e9s 3ebn 3r24 4tww 4twy 4wy3 4zuh 5b6o 5c5n 5c5o 5c8s 5c8t 5c8u 5e6j 5f22 5tl6 5tl7
        R1A_CVHSA | P0C6U81o5s 1p76 1p9t 1pa5 1puk 1q1x 1q2w 1qz8 1uj1 1uk2 1uk3 1uk4 1uw7 1wof 1ysy 1z1i 1z1j 2a5a 2a5i 2a5k 2acf 2ahm 2aj5 2alv 2amd 2amq 2bx3 2bx4 2c3s 2d2d 2duc 2fav 2fe8 2fyg 2g1f 2g9t 2ga6 2gdt 2gri 2gt7 2gt8 2gtb 2gx4 2gz7 2gz8 2gz9 2h2z 2hob 2hsx 2idy 2jzd 2jze 2jzf 2k87 2kaf 2kqv 2kqw 2kys 2liz 2op9 2ozk 2pwx 2qc2 2qcy 2qiq 2rhb 2rnk 2w2g 2wct 2z3c 2z3d 2z3e 2z94 2z9g 2z9j 2z9k 2z9l 2zu4 2zu5 3atw 3avz 3aw0 3aw1 3d62 3e91 3e9s 3ea7 3ea8 3ea9 3eaj 3ee7 3f9e 3f9f 3f9g 3f9h 3fzd 3iwm 3m3s 3m3t 3m3v 3mj5 3r24 3sn8 3sna 3snb 3snc 3snd 3sne 3szn 3tit 3tiu 3tns 3tnt 3v3m 3vb3 3vb4 3vb5 3vb6 3vb7 4hi3 4m0w 4mds 4mm3 4ovz 4ow0 5f22

(-) Related Entries Specified in the PDB File

2q6d 2q6f