Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
ASCOP2B SuperfamilyS-adenosyl-L-methionine-dependent methyltransferases 8092457 3000118 SCOP2B (2022-06-29)
CSCOP2B SuperfamilyS-adenosyl-L-methionine-dependent methyltransferases 8092457 3000118 SCOP2B (2022-06-29)
BSCOP2B SuperfamilySARS coronavirus NSP10-like 8092459 3000547 SCOP2B (2022-06-29)
DSCOP2B SuperfamilySARS coronavirus NSP10-like 8092459 3000547 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
ANSP13e6w75A1 A: a/b three-layered sandwichesX: Rossmann-likeH: Rossmann-relatedT: S-adenosyl-L-methionine-dependent methyltransferasesF: NSP13ECOD (1.6)
CNSP13e6w75C1 A: a/b three-layered sandwichesX: Rossmann-likeH: Rossmann-relatedT: S-adenosyl-L-methionine-dependent methyltransferasesF: NSP13ECOD (1.6)
BNSP10e6w75B1 A: few secondary structure elementsX: Coronavirus NSP10-like (From Topology)H: Coronavirus NSP10-like (From Topology)T: Coronavirus NSP10-likeF: NSP10ECOD (1.6)
DNSP10e6w75D1 A: few secondary structure elementsX: Coronavirus NSP10-like (From Topology)H: Coronavirus NSP10-like (From Topology)T: Coronavirus NSP10-likeF: NSP10ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
A3.40.50.150 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold Vaccinia Virus protein VP39CATH (utative)
C3.40.50.150 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold Vaccinia Virus protein VP39CATH (utative)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A, C
PF06460Coronavirus 2'-O-methyltransferase (CoV_Methyltr_2)Coronavirus 2'-O-methyltransferaseThis domain covers the NSP16 region of the coronavirus polyprotein. The SARS-CoV RNA cap SAM-dependent (nucleoside-2'-O-)-methyltransferase (2'-O-MTase) is a heterodimer comprising SARS-CoV nsp10 and nsp16. When bound to nsp10, nsp16 is active as a t ...This domain covers the NSP16 region of the coronavirus polyprotein. The SARS-CoV RNA cap SAM-dependent (nucleoside-2'-O-)-methyltransferase (2'-O-MTase) is a heterodimer comprising SARS-CoV nsp10 and nsp16. When bound to nsp10, nsp16 is active as a type-0 RNA cap-dependent 2'-O-MTase, ie., active only when the cap guanine is methylated at its N7 position. Nsp10 binds to nsp16 through an activation surface area in nsp10, and the resulting complex exhibits RNA cap (nucleoside-2'-O)-methyltransferase activity. Nsp10 is a double zinc finger protein together with nsp4, nsp5, nsp12, nsp14, and nsp16, nsp10 has been found to be essential in the assembly of a functional replication/transcription complex. NSP16 plays a key role in viral replication as it is involved in immune response evasion through the 2'-O-methylation of coronavirus RNA, which is essential for preventing recognition by the host. It mimics the human protein CMTr1 and, unlike CMTr1, it requires NSP10 as a binding partner to activate its enzymatic activity [4]. Nsp16 adopts a typical fold of the S-adenosylmethionine-dependent methyltransferase (SAM) family as defined initially for the catechol O-MTase but it lacks several elements of the canonical MTase fold, such as helices B and C. The nsp16 topology matches those of dengue virus NS5 N-terminal domain and of vaccinia virus VP39 MTases [1,2, 3]. Structural analysis in NSP16 from SARS-CoV-2 identified a cryptic pocket (also present in other coronavirus such as SARS-CoV-1 and MERS) not present in human CMTr1, and the fact that NSP16 is one of the most conserved proteins of SARS-CoV-2 and related viruses, make it an interesting target for developing new antiviral treatment for COVID-19 and other diseases caused by coronaviruses [5].
Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A, C
2'-O-methyltransferase
B, D
Non-structural protein 10

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
A, C
IPR022733DPUP/SUD, C-terminal, betacoronavirusDomain
A, C
IPR042515Non-structural protein NSP15, N-terminal domain superfamily, coronavirusHomologous Superfamily
A, C
IPR043174Non-structural protein NSP15, middle domain superfamilyHomologous Superfamily
A, C
IPR044315Nonstructural protein 14, betacoronavirusDomain
A, C
IPR038123Non-structural protein NSP4, C-terminal superfamily, coronavirusHomologous Superfamily
A, C
IPR042570Non-structural protein NSP3, nucleic acid-binding domain superfamily, betacoronavirusHomologous Superfamily
A, C
IPR043178Papain-like protease, thumb domain superfamily, coronavirusHomologous Superfamily
A, C
IPR046441RNA-dependent RNA polymerase, coronavirusDomain
A, C
IPR044863Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domainDomain
A, C
IPR044343Nonstructural protein 13, 1B domain, coronavirusDomain
A, C
IPR038166Polyprotein cleavage domain PL2pro superfamily, betacoronavirusHomologous Superfamily
A, C
IPR037227Endoribonuclease EndoU-likeHomologous Superfamily
A, C
IPR027352Nonstructural protein 13, zinc-binding domain, coronavirus-likeDomain
A, C
IPR009003Peptidase S1, PA clanHomologous Superfamily
A, C
IPR013016Peptidase C16, coronavirusDomain
A, C
IPR009466Non-structural protein 14, coronavirusDomain
A, C
IPR044357NSP3, first ubiquitin-like (Ubl) domain, coronavirusDomain
A, C
IPR046436Nidovirus 3'-5' exoribonuclease domainDomain
A, C
IPR047570NSP12, interface domain, coronavirusDomain
A, C
IPR018995RNA synthesis protein NSP10, coronavirusDomain
A, C
IPR043615Nonstructural protein 2, N-terminal domain, coronavirusDomain
A, C
IPR050534Coronaviruses polyprotein 1abFamily
A, C
IPR043177Papain-like protease, N-terminal domain superfamily, coronavirusHomologous Superfamily
A, C
IPR043606Coronavirus replicase NSP15, N-terminal oligomerizationDomain
A, C
IPR044330Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirusDomain
A, C
IPR041679DNA2/NAM7 helicase-like, C-terminalDomain
A, C
IPR024375Non-structural protein NSP3, SUD-M domain, betacoronavirusDomain
A, C
IPR014828Non-structural protein NSP7, coronavirusDomain
A, C
IPR043503Papain-like viral protease, palm and finger domains, coronavirusHomologous Superfamily
A, C
IPR014829Non-structural protein NSP8, coronavirusDomain
A, C
IPR036499Non-structural protein NSP9 superfamily, coronavirusHomologous Superfamily
A, C
IPR029063S-adenosyl-L-methionine-dependent methyltransferase superfamilyHomologous Superfamily
A, C
IPR044389Non-structural protein 2, SARS-CoV-likeDomain
A, C
IPR043502DNA/RNA polymerase superfamilyHomologous Superfamily
A, C
IPR008740Peptidase C30, coronavirusDomain
A, C
IPR036333RNA synthesis protein NSP10 superfamily, coronavirusHomologous Superfamily
A, C
IPR047573Non-structural protein 2, middle domain, coronavirusDomain
A, C
IPR049894Coronavirus NSP3, 3Ecto domainDomain
A, C
IPR043472Macro domain-likeHomologous Superfamily
A, C
IPR043609NendoU domain, nidovirusDomain
A, C
IPR032592Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirusDomain
A, C
IPR043613Non-structural protein 2, C-terminal domain, coronavirusDomain
A, C
IPR038083Non-structural protein NSP3A domain-like superfamilyHomologous Superfamily
A, C
IPR043504Peptidase S1, PA clan, chymotrypsin-like foldHomologous Superfamily
A, C
IPR044351RNA-dependent RNA polymerase, SARS-CoV-likeDomain
A, C
IPR024358Non-structural protein NSP3, N-terminal, betacoronavirusDomain
A, C
IPR048673Nonstructural protein 13, stalk domain, coronavirusDomain
A, C
IPR046435NSP14, guanine-N7-methyltransferase domain, coronavirusDomain
A, C
IPR009469RNA-dependent RNA polymerase, N-terminal, coronavirusDomain
A, C
IPR043611Coronavirus replicase NSP3, C-terminalDomain
A, C
IPR044864Non-structural protein NSP3, SUD-N (Mac2) domain, betacoronavirusDomain
A, C
IPR047566Coronavirus replicase NSP3, Y domainDomain
A, C
IPR048672Nonstructural protein 13, zinc-binding domain, coronavirusDomain
A, C
IPR043612Non-structural protein NSP4, N-terminal, coronavirusDomain
A, C
IPR027417P-loop containing nucleoside triphosphate hydrolaseHomologous Superfamily
A, C
IPR043608Nonstructural protein 15, middle domain, coronavirusDomain
A, C
IPR044353NSP3, second ubiquitin-like (Ubl) domain, coronavirusDomain
A, C
IPR037204Non-structural protein NSP7 superfamily, coronavirusHomologous Superfamily
A, C
IPR046443NSP1, globular domain, alpha/betacoronavirusDomain
A, C
IPR043610Non-structural protein 6, coronavirusDomain
A, C
IPR027351(+) RNA virus helicase core domainDomain
A, C
IPR044322Nonstructural protein 15, middle domain, alpha/betacoronavirusDomain
A, C
IPR009461Non-structural protein NSP16, coronavirus-likeDomain
A, C
IPR043477Peptidase C30, domain 3, coronavirusHomologous Superfamily
A, C
IPR043478Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirusHomologous Superfamily
A, C
IPR038400Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirusHomologous Superfamily
A, C
IPR046442NSP1, C-terminal domain, betacoronavirusDomain
A, C
IPR001205RNA-directed RNA polymerase, C-terminal domainDomain
A, C
IPR044401NSP15, NendoU domain, coronavirusDomain
A, C
IPR014822Non-structural protein NSP9, coronavirusDomain
A, C
IPR038030NSP1 globular domain superfamily, betacoronavirusHomologous Superfamily
A, C
IPR021590NSP1, globular domain, betacoronavirusDomain
A, C
IPR044367Non-structural protein 6, betacoronavirusDomain
A, C
IPR037230Non-structural protein NSP8 superfamily, coronavirusHomologous Superfamily
A, C
IPR046440Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domainDomain
A, C
IPR032505Non-structural protein NSP4, C-terminal, coronavirusDomain
A, C
IPR046438Nidovirus 2-O-methyltransferaseDomain
A, C
IPR002589Macro domainDomain
A, C
IPR047567Non-structural protein NSP3, group 2-specific marker domain, betacoronavirusDomain
A, C
IPR044371Non-structural protein 3, X-domain-likeDomain
A, C
IPR007094RNA-directed RNA polymerase, catalytic domainDomain
B, D
IPR022733DPUP/SUD, C-terminal, betacoronavirusDomain
B, D
IPR042515Non-structural protein NSP15, N-terminal domain superfamily, coronavirusHomologous Superfamily
B, D
IPR043174Non-structural protein NSP15, middle domain superfamilyHomologous Superfamily
B, D
IPR044315Nonstructural protein 14, betacoronavirusDomain
B, D
IPR038123Non-structural protein NSP4, C-terminal superfamily, coronavirusHomologous Superfamily
B, D
IPR042570Non-structural protein NSP3, nucleic acid-binding domain superfamily, betacoronavirusHomologous Superfamily
B, D
IPR043178Papain-like protease, thumb domain superfamily, coronavirusHomologous Superfamily
B, D
IPR046441RNA-dependent RNA polymerase, coronavirusDomain
B, D
IPR044863Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domainDomain
B, D
IPR044343Nonstructural protein 13, 1B domain, coronavirusDomain
B, D
IPR038166Polyprotein cleavage domain PL2pro superfamily, betacoronavirusHomologous Superfamily
B, D
IPR037227Endoribonuclease EndoU-likeHomologous Superfamily
B, D
IPR027352Nonstructural protein 13, zinc-binding domain, coronavirus-likeDomain
B, D
IPR009003Peptidase S1, PA clanHomologous Superfamily
B, D
IPR013016Peptidase C16, coronavirusDomain
B, D
IPR009466Non-structural protein 14, coronavirusDomain
B, D
IPR044357NSP3, first ubiquitin-like (Ubl) domain, coronavirusDomain
B, D
IPR046436Nidovirus 3'-5' exoribonuclease domainDomain
B, D
IPR047570NSP12, interface domain, coronavirusDomain
B, D
IPR018995RNA synthesis protein NSP10, coronavirusDomain
B, D
IPR043615Nonstructural protein 2, N-terminal domain, coronavirusDomain
B, D
IPR050534Coronaviruses polyprotein 1abFamily
B, D
IPR043177Papain-like protease, N-terminal domain superfamily, coronavirusHomologous Superfamily
B, D
IPR043606Coronavirus replicase NSP15, N-terminal oligomerizationDomain
B, D
IPR044330Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirusDomain
B, D
IPR041679DNA2/NAM7 helicase-like, C-terminalDomain
B, D
IPR024375Non-structural protein NSP3, SUD-M domain, betacoronavirusDomain
B, D
IPR014828Non-structural protein NSP7, coronavirusDomain
B, D
IPR043503Papain-like viral protease, palm and finger domains, coronavirusHomologous Superfamily
B, D
IPR014829Non-structural protein NSP8, coronavirusDomain
B, D
IPR036499Non-structural protein NSP9 superfamily, coronavirusHomologous Superfamily
B, D
IPR029063S-adenosyl-L-methionine-dependent methyltransferase superfamilyHomologous Superfamily
B, D
IPR044389Non-structural protein 2, SARS-CoV-likeDomain
B, D
IPR043502DNA/RNA polymerase superfamilyHomologous Superfamily
B, D
IPR008740Peptidase C30, coronavirusDomain
B, D
IPR036333RNA synthesis protein NSP10 superfamily, coronavirusHomologous Superfamily
B, D
IPR047573Non-structural protein 2, middle domain, coronavirusDomain
B, D
IPR049894Coronavirus NSP3, 3Ecto domainDomain
B, D
IPR043472Macro domain-likeHomologous Superfamily
B, D
IPR043609NendoU domain, nidovirusDomain
B, D
IPR032592Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirusDomain
B, D
IPR043613Non-structural protein 2, C-terminal domain, coronavirusDomain
B, D
IPR038083Non-structural protein NSP3A domain-like superfamilyHomologous Superfamily
B, D
IPR043504Peptidase S1, PA clan, chymotrypsin-like foldHomologous Superfamily
B, D
IPR044351RNA-dependent RNA polymerase, SARS-CoV-likeDomain
B, D
IPR024358Non-structural protein NSP3, N-terminal, betacoronavirusDomain
B, D
IPR048673Nonstructural protein 13, stalk domain, coronavirusDomain
B, D
IPR046435NSP14, guanine-N7-methyltransferase domain, coronavirusDomain
B, D
IPR009469RNA-dependent RNA polymerase, N-terminal, coronavirusDomain
B, D
IPR043611Coronavirus replicase NSP3, C-terminalDomain
B, D
IPR044864Non-structural protein NSP3, SUD-N (Mac2) domain, betacoronavirusDomain
B, D
IPR047566Coronavirus replicase NSP3, Y domainDomain
B, D
IPR048672Nonstructural protein 13, zinc-binding domain, coronavirusDomain
B, D
IPR043612Non-structural protein NSP4, N-terminal, coronavirusDomain
B, D
IPR027417P-loop containing nucleoside triphosphate hydrolaseHomologous Superfamily
B, D
IPR043608Nonstructural protein 15, middle domain, coronavirusDomain
B, D
IPR044353NSP3, second ubiquitin-like (Ubl) domain, coronavirusDomain
B, D
IPR037204Non-structural protein NSP7 superfamily, coronavirusHomologous Superfamily
B, D
IPR046443NSP1, globular domain, alpha/betacoronavirusDomain
B, D
IPR043610Non-structural protein 6, coronavirusDomain
B, D
IPR027351(+) RNA virus helicase core domainDomain
B, D
IPR044322Nonstructural protein 15, middle domain, alpha/betacoronavirusDomain
B, D
IPR009461Non-structural protein NSP16, coronavirus-likeDomain
B, D
IPR043477Peptidase C30, domain 3, coronavirusHomologous Superfamily
B, D
IPR043478Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirusHomologous Superfamily
B, D
IPR038400Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirusHomologous Superfamily
B, D
IPR046442NSP1, C-terminal domain, betacoronavirusDomain
B, D
IPR001205RNA-directed RNA polymerase, C-terminal domainDomain
B, D
IPR044401NSP15, NendoU domain, coronavirusDomain
B, D
IPR014822Non-structural protein NSP9, coronavirusDomain
B, D
IPR038030NSP1 globular domain superfamily, betacoronavirusHomologous Superfamily
B, D
IPR021590NSP1, globular domain, betacoronavirusDomain
B, D
IPR044367Non-structural protein 6, betacoronavirusDomain
B, D
IPR037230Non-structural protein NSP8 superfamily, coronavirusHomologous Superfamily
B, D
IPR046440Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domainDomain
B, D
IPR032505Non-structural protein NSP4, C-terminal, coronavirusDomain
B, D
IPR046438Nidovirus 2-O-methyltransferaseDomain
B, D
IPR002589Macro domainDomain
B, D
IPR047567Non-structural protein NSP3, group 2-specific marker domain, betacoronavirusDomain
B, D
IPR044371Non-structural protein 3, X-domain-likeDomain
B, D
IPR007094RNA-directed RNA polymerase, catalytic domainDomain