6XCN

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


Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
ASpike_NTDe6xcnA3 A: beta sandwichesX: jelly-rollH: Concanavalin A-likeT: Concanavalin A-like lectins/glucanasesF: Spike_NTDECOD (1.6)
ASpike_rec_bind_1e6xcnA1 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: Spike_rec_bind_1ECOD (1.6)
ASpike_rec_binde6xcnA2 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: Spike_rec_bindECOD (1.6)
ACorona_S2e6xcnA4 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: Corona_S2ECOD (1.6)
B [auth C]Spike_NTDe6xcnC2 A: beta sandwichesX: jelly-rollH: Concanavalin A-likeT: Concanavalin A-like lectins/glucanasesF: Spike_NTDECOD (1.6)
B [auth C]Spike_rec_bind_1e6xcnC3 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: Spike_rec_bind_1ECOD (1.6)
B [auth C]Spike_rec_binde6xcnC4 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: Spike_rec_bindECOD (1.6)
B [auth C]Corona_S2e6xcnC1 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: Corona_S2ECOD (1.6)
C [auth E]Spike_NTDe6xcnE1 A: beta sandwichesX: jelly-rollH: Concanavalin A-likeT: Concanavalin A-like lectins/glucanasesF: Spike_NTDECOD (1.6)
C [auth E]Spike_rec_bind_1e6xcnE2 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: Spike_rec_bind_1ECOD (1.6)
C [auth E]Spike_rec_binde6xcnE3 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: Spike_rec_bindECOD (1.6)
C [auth E]Corona_S2e6xcnE4 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: Corona_S2ECOD (1.6)
D [auth B]V-set_8e6xcnB1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-set_8ECOD (1.6)
E [auth F]V-set_8e6xcnF1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-set_8ECOD (1.6)
F [auth H]V-set_8e6xcnH1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-set_8ECOD (1.6)
G [auth D]V-set_3e6xcnD1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-set_3ECOD (1.6)
H [auth G]V-set_3e6xcnG1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-set_3ECOD (1.6)
I [auth L]V-set_3e6xcnL1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-set_3ECOD (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 (202449-0)
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 (202449-0)

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 (2024-12-13)
G [auth D],
H [auth G],
I [auth L]
Light ChainIGLV2 Lambdaspike glycoproteinSAbDab (2024-12-13)

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---