Domain Annotation: SCOP/SCOPe Classification SCOP Database Homepage

ChainsDomain InfoClassFoldSuperfamilyFamilyDomainSpeciesProvenance Source (Version)
A [auth S]d3bgfs_ Alpha and beta proteins (a+b) SARS receptor-binding domain-like SARS receptor-binding domain-like SARS receptor-binding domain-like Spike protein S1 SARS-CoV (Severe acute respiratory syndrome-related coronavirus ) [TaxId: 694009 ], SCOPe (2.08)
B [auth A]d3bgfa_ Alpha and beta proteins (a+b) SARS receptor-binding domain-like SARS receptor-binding domain-like SARS receptor-binding domain-like Spike protein S1 SARS-CoV (Severe acute respiratory syndrome-related coronavirus ) [TaxId: 694009 ], SCOPe (2.08)
C [auth L]d3bgfl2 All beta proteins Immunoglobulin-like beta-sandwich Immunoglobulin C1 set domains (antibody constant domain-like) automated matches (Mus musculus ) [TaxId: 10090 ], SCOPe (2.08)
C [auth L]d3bgfl1 All beta proteins Immunoglobulin-like beta-sandwich Immunoglobulin automated matches automated matches (Mus musculus ) [TaxId: 10090 ], SCOPe (2.08)
E [auth C]d3bgfc2 All beta proteins Immunoglobulin-like beta-sandwich Immunoglobulin C1 set domains (antibody constant domain-like) automated matches (Mus musculus ) [TaxId: 10090 ], SCOPe (2.08)
E [auth C]d3bgfc1 All beta proteins Immunoglobulin-like beta-sandwich Immunoglobulin automated matches automated matches (Mus musculus ) [TaxId: 10090 ], SCOPe (2.08)
D [auth H]d3bgfh_ All beta proteins Immunoglobulin-like beta-sandwich Immunoglobulin automated matches automated matches (Mus musculus ) [TaxId: 10090 ], SCOPe (2.08)
F [auth B]d3bgfb_ All beta proteins Immunoglobulin-like beta-sandwich Immunoglobulin automated matches automated matches (Mus musculus ) [TaxId: 10090 ], SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
A [auth S]SCOP2B SuperfamilySARS coronavirus receptor-binding domain-like8041894 3001706 SCOP2B (2022-06-29)
B [auth A]SCOP2B SuperfamilySARS coronavirus receptor-binding domain-like8041894 3001706 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
A [auth S]PF09408e3bgfS1 A: a+b three layersX: Coronavirus spike protein receptor-binding domain (From Homology)H: Coronavirus spike protein receptor-binding domainT: Beta-coronavirus spike protein receptor-binding domainF: PF09408ECOD (1.6)
B [auth A]PF09408e3bgfA1 A: a+b three layersX: Coronavirus spike protein receptor-binding domain (From Homology)H: Coronavirus spike protein receptor-binding domainT: Beta-coronavirus spike protein receptor-binding domainF: PF09408ECOD (1.6)
C [auth L]PF07654e3bgfL2 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: PF07654ECOD (1.6)
C [auth L]PF07686e3bgfL1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: PF07686ECOD (1.6)
E [auth C]PF07654e3bgfC2 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: PF07654ECOD (1.6)
E [auth C]PF07686e3bgfC1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: PF07686ECOD (1.6)
D [auth H]PF07654e3bgfH2 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: PF07654ECOD (1.6)
D [auth H]PF07686e3bgfH1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: PF07686ECOD (1.6)
F [auth B]PF07654e3bgfB2 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: PF07654ECOD (1.6)
F [auth B]PF07686e3bgfB1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: PF07686ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

IMGT Antibody Annotation IMGT Database Homepage

ChainProtein NameDescriptionOrganism NameGene Allele Name(s)Domain Name(s)Receptor TypeReceptor DescriptionProvenance Source
C [auth L],
E [auth C]
Fab F26G19 L-KAPPA Mus musculus (house mouse) IGKV9-124*01, IGKJ1*01, IGKJ1*02, IGKC*01, IGKC*02 V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA IG FAB-GAMMA-2C_KAPPA IMGT (202411-0)
D [auth H],
F [auth B]
Fab F26G19 VH-CH1 Mus musculus (house mouse) IGHV1-5*01, IGHJ4*01, IGHG2A*01, IGHG2A*02 V-DOMAIN VH, C-DOMAIN CH1 IG FAB-GAMMA-2C_KAPPA IMGT (202411-0)

SAbDab Antibody Annotation SAbDab Database Homepage

ChainChain ClassChain SubclassChain TypeAntigen Name(s) Provenance Source
C [auth L],
E [auth C]
Light ChainIGKV9 Kappaspike protein s1SAbDab (2024-03-22)
D [auth H],
F [auth B]
Heavy ChainIGHV1 -spike protein s1SAbDab (2024-03-22)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A [auth S],
B [auth A]
PF16451Betacoronavirus-like spike glycoprotein S1, N-terminal (bCoV_S1_N)Betacoronavirus-like spike glycoprotein S1, N-terminalThis entry represents the N-terminal domain of the betacoronavirus-like trimeric spike glycoprotein. The distal S1 subunit of the coronavirus spike protein is responsible for receptor binding. S1 contains two domains; an N-terminal galectin-like doma ...This entry represents the N-terminal domain of the betacoronavirus-like trimeric spike glycoprotein. The distal S1 subunit of the coronavirus spike protein is responsible for receptor binding. S1 contains two domains; an N-terminal galectin-like domain (NTD) and a receptor-binding domain (S1 RBD) also referred to as the S1 CTD or domain B. Either the S1 NTD or S1 RBD, or occasionally both, are involved in binding to host receptors. S1 NTD is located on the side of the spike trimer and mainly recognises sugar receptors [2]. For many betacoronaviruses (b-CoVs), for example mouse hepatitis virus (MHV), the RBD is located in the NTD. The structure of the MHV S1 NTD showed the same fold as human galectins (galactose-binding lectin), however it does not bind any sugar; instead, it binds to the carcinoembryonic antigen cell-adhesion molecule CEACAM1) through protein-protein interactions [2]. All three CEACAM21a-binding sites in MHV spikes can be fully occupied by CEACAM1a. It has been shown that CEACAM1a binding to the MHV spike weakens the interactions between S1 and S2 and facilitates the proteolysis of the spike protein and dissociation of S1 [2]. The homologous bovine CoV (BCov) S1 NTD also possesses a galectin fold but binds to sialic acid-containing moieties on host cell membranes, as does the NTD of three other group A b-Covs, namely human CoV (HCoV) OC43, avian b-CoV, and infectious bronchitis virus (IBV) [3]. Despite the S1 NTD of human respiratory b-CoV HKU1 being highly homologous to the NTDs of MHV and bovine CoV, it does not bind to either sugar or human carcinoembryonic antigen-related cell adhesion molecules (CEACAMs) and the RBD is found instead in the S1 RBD domain [3].
Domain
A [auth S],
B [auth A]
PF09408Betacoronavirus spike glycoprotein S1, receptor binding (bCoV_S1_RBD)Betacoronavirus spike glycoprotein S1, receptor bindingThis entry represents the receptor binding domain (S1 RBD) of the betacoronavirus spike glycoprotein. The spike glycoprotein is arranged in trimers on the surface of the viral membrane and is essential for viral entry. The spike protein is transla ...This entry represents the receptor binding domain (S1 RBD) of the betacoronavirus spike glycoprotein. The spike glycoprotein is arranged in trimers on the surface of the viral membrane and is essential for viral entry. The spike protein is translated as a large polypeptide that is subsequently cleaved to the distal S1, responsible for receptor binding, and the membrane-anchored S2 responsible for membrane fusion [1]. The coronavirus (SARS-CoV) S1 subunit is composed of two distinct domains: an N-terminal domain (S1 NTD) and a receptor-binding domain (S1 RBD) also referred to as the S1 CTD or domain B. Each of these domains have been implicated in binding to host receptors. However, most coronaviruses are not known to utilise both the S1 NTD and S1 RBD for viral entry [2]. SARS-CoV makes use of its S1 RBD to bind to the human angiotensin-converting enzyme 2 (ACE2) as its host receptor [3,4].
Domain
C [auth L],
E [auth C]
PF07686Immunoglobulin V-set domain (V-set)Immunoglobulin V-set domainThis domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.Domain
C [auth L],
E [auth C]
PF07654Immunoglobulin C1-set domain (C1-set)Immunoglobulin C1-set domain- Domain
D [auth H],
F [auth B]
PF07686Immunoglobulin V-set domain (V-set)Immunoglobulin V-set domainThis domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A [auth S],
B [auth A]
Spike protein S1
C [auth L],
E [auth C]
F26G19 Fab- - -
D [auth H],
F [auth B]
F26G19 Fab- - -

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
A [auth S],
B [auth A]
IPR044873Spike glycoprotein S2, coronavirus, heptad repeat 1Domain
A [auth S],
B [auth A]
IPR018548Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirusDomain
A [auth S],
B [auth A]
IPR044341Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-likeDomain
A [auth S],
B [auth A]
IPR032500Spike glycoprotein S1, N-terminal domain, betacoronavirus-likeDomain
A [auth S],
B [auth A]
IPR042578Spike glycoprotein, betacoronavirusFamily
A [auth S],
B [auth A]
IPR036326Spike S1 subunit, receptor binding domain superfamily, betacoronavirusHomologous Superfamily
A [auth S],
B [auth A]
IPR043002Spike glycoprotein, N-terminal domain superfamilyHomologous Superfamily
A [auth S],
B [auth A]
IPR044874Spike glycoprotein S2, coronavirus, heptad repeat 2Domain
A [auth S],
B [auth A]
IPR043473Spike glycoprotein S2 superfamily, coronavirusHomologous Superfamily
A [auth S],
B [auth A]
IPR043607Coronavirus spike glycoprotein S1, C-terminalDomain
A [auth S],
B [auth A]
IPR002552Spike glycoprotein S2, coronavirusDomain
A [auth S],
B [auth A]
IPR044370Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoVDomain
C [auth L],
E [auth C]
IPR003597Immunoglobulin C1-setDomain
C [auth L],
E [auth C]
IPR013783Immunoglobulin-like foldHomologous Superfamily
C [auth L],
E [auth C]
IPR036179Immunoglobulin-like domain superfamilyHomologous Superfamily
C [auth L],
E [auth C]
IPR003599Immunoglobulin subtypeDomain
C [auth L],
E [auth C]
IPR013106Immunoglobulin V-set domainDomain
C [auth L],
E [auth C]
IPR007110Immunoglobulin-like domainDomain
C [auth L],
E [auth C]
IPR003006Immunoglobulin/major histocompatibility complex, conserved siteConserved Site
D [auth H],
F [auth B]
IPR013783Immunoglobulin-like foldHomologous Superfamily
D [auth H],
F [auth B]
IPR036179Immunoglobulin-like domain superfamilyHomologous Superfamily
D [auth H],
F [auth B]
IPR003599Immunoglobulin subtypeDomain
D [auth H],
F [auth B]
IPR013106Immunoglobulin V-set domainDomain
D [auth H],
F [auth B]
IPR007110Immunoglobulin-like domainDomain