6XCN

Structure of the SARS-CoV-2 spike glycoprotein in complex with the C105 neutralizing antibody Fab fragment (state 2)


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
C [auth E]SCOP2B SuperfamilyCoronavirus spike S2 glycoprotein connector domain-like8092473 3002562 SCOP2B (2022-06-29)
C [auth E]SCOP2B SuperfamilySARS coronavirus receptor-binding domain-like8092467 3001706 SCOP2B (2022-06-29)
C [auth E]SCOP2B SuperfamilyCoronavirus S2 glycoprotein stalk-like8092471 3000282 SCOP2B (2022-06-29)
C [auth E]SCOP2B SuperfamilyCoronavirus S1 glycoprotein domain C-like8092661 3002615 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyCoronavirus S1 glycoprotein domain C-like8092661 3002615 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyCoronavirus spike S2 glycoprotein connector domain-like8092473 3002562 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyCoronavirus S2 glycoprotein stalk-like8092471 3000282 SCOP2B (2022-06-29)
ASCOP2B SuperfamilySARS coronavirus receptor-binding domain-like8092467 3001706 SCOP2B (2022-06-29)
B [auth C]SCOP2B SuperfamilyCoronavirus spike S2 glycoprotein connector domain-like8092473 3002562 SCOP2B (2022-06-29)
B [auth C]SCOP2B SuperfamilyCoronavirus S1 glycoprotein domain C-like8092661 3002615 SCOP2B (2022-06-29)
B [auth C]SCOP2B SuperfamilyCoronavirus S2 glycoprotein stalk-like8092471 3000282 SCOP2B (2022-06-29)
B [auth C]SCOP2B SuperfamilySARS coronavirus receptor-binding domain-like8092467 3001706 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
C [auth E]PF16451e6xcnE1 A: beta sandwichesX: jelly-rollH: Concanavalin A-likeT: Concanavalin A-like lectins/glucanasesF: PF16451ECOD (1.6)
C [auth E]PF19209e6xcnE2 A: beta complex topologyX: Beta domain of coronavirus spike glycoprotein (From Topology)H: Beta domain of coronavirus spike glycoprotein (From Topology)T: Beta domain of coronavirus spike glycoproteinF: PF19209ECOD (1.6)
C [auth E]PF09408e6xcnE3 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 E]PF01601e6xcnE4 A: a+b complex topologyX: S2 subunit of coronavirus spike glycoprotein (From Topology)H: S2 subunit of coronavirus spike glycoprotein (From Topology)T: S2 subunit of coronavirus spike glycoproteinF: PF01601ECOD (1.6)
APF16451e6xcnA3 A: beta sandwichesX: jelly-rollH: Concanavalin A-likeT: Concanavalin A-like lectins/glucanasesF: PF16451ECOD (1.6)
APF19209e6xcnA1 A: beta complex topologyX: Beta domain of coronavirus spike glycoprotein (From Topology)H: Beta domain of coronavirus spike glycoprotein (From Topology)T: Beta domain of coronavirus spike glycoproteinF: PF19209ECOD (1.6)
APF09408e6xcnA2 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)
APF01601e6xcnA4 A: a+b complex topologyX: S2 subunit of coronavirus spike glycoprotein (From Topology)H: S2 subunit of coronavirus spike glycoprotein (From Topology)T: S2 subunit of coronavirus spike glycoproteinF: PF01601ECOD (1.6)
B [auth C]PF16451e6xcnC2 A: beta sandwichesX: jelly-rollH: Concanavalin A-likeT: Concanavalin A-like lectins/glucanasesF: PF16451ECOD (1.6)
B [auth C]PF19209e6xcnC3 A: beta complex topologyX: Beta domain of coronavirus spike glycoprotein (From Topology)H: Beta domain of coronavirus spike glycoprotein (From Topology)T: Beta domain of coronavirus spike glycoproteinF: PF19209ECOD (1.6)
B [auth C]PF09408e6xcnC4 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 C]PF01601e6xcnC1 A: a+b complex topologyX: S2 subunit of coronavirus spike glycoprotein (From Topology)H: S2 subunit of coronavirus spike glycoprotein (From Topology)T: S2 subunit of coronavirus spike glycoproteinF: PF01601ECOD (1.6)
E [auth F]PF07686e6xcnF1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: PF07686ECOD (1.6)
D [auth B]PF07686e6xcnB1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: PF07686ECOD (1.6)
F [auth H]PF07686e6xcnH1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: PF07686ECOD (1.6)
G [auth D]PF07686e6xcnD1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: PF07686ECOD (1.6)
I [auth L]PF07686e6xcnL1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: PF07686ECOD (1.6)
H [auth G]PF07686e6xcnG1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: PF07686ECOD (1.6)

IMGT Antibody Annotation IMGT Database Homepage

ChainProtein NameDescriptionOrganism NameGene Allele Name(s)Domain Name(s)Receptor TypeReceptor DescriptionProvenance Source
D [auth B],
E [auth F],
F [auth H]
Fab C105, anti-SARS-CoV-2, neutralizing VH-CH1 Homo sapiens (human) IGHV3-53*01, IGHJ4*01, IGHJ4*02, IGHJ4*03, IGHJ5*01, IGHJ6-3*01, IGHG1*03, IGHG1*08, IGHG1*06 V-DOMAIN VH, C-DOMAIN CH1 IG FAB-GAMMA-1_LAMBDA IMGT (202409-0)
G [auth D],
H [auth G],
I [auth L]
Fab C105, anti-SARS-CoV-2, neutralizing L-LAMBDA Homo sapiens (human) IGLV2-8*01, IGLJ2*01, IGLJ3*01, IGLC2*01, IGLC2*02, IGLC3*04 V-DOMAIN V-LAMBDA, C-DOMAIN C-LAMBDA IG FAB-GAMMA-1_LAMBDA IMGT (202409-0)

SAbDab Antibody Annotation SAbDab Database Homepage

ChainChain ClassChain SubclassChain TypeAntigen Name(s) Provenance Source
D [auth B],
E [auth F],
F [auth H]
Heavy ChainIGHV3 -spike glycoproteinSAbDab (2024-03-08)
G [auth D],
H [auth G],
I [auth L]
Light ChainIGLV2 Lambdaspike glycoproteinSAbDab (2024-03-08)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A,
B [auth C],
C [auth E]
PF01601Coronavirus spike glycoprotein S2 (CoV_S2)Coronavirus spike glycoprotein S2- Family
A,
B [auth C],
C [auth E]
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,
B [auth C],
C [auth E]
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
A,
B [auth C],
C [auth E]
PF19209Coronavirus spike glycoprotein S1, C-terminal (CoV_S1_C)Coronavirus spike glycoprotein S1, C-terminalThis entry represents a domain found at the C-terminus of the Coronavirus S1 protein. It is found across a range of alpha, beta and gamma coronaviruses. This small all beta stranded domain is known as subdomain 2 in the structure of the porcine epide ...This entry represents a domain found at the C-terminus of the Coronavirus S1 protein. It is found across a range of alpha, beta and gamma coronaviruses. This small all beta stranded domain is known as subdomain 2 in the structure of the porcine epidemic diarrhea virus spike protein [1].
Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A,
B [auth C],
C [auth E]
Spike glycoprotein
D [auth B],
E [auth F],
F [auth H]
C105 Fab Heavy Chain---
G [auth D],
H [auth G],
I [auth L]
C105 Fab Light Chain---