Annotations: 9KVD

Cryo-EM structure of SARS-CoV-2 prototype spike protein in complex with triple-nAb 3G5, 4H5 and 4C11

External Resource: Annotation

Domain Annotation: ECOD Classification
SAbDab Antibody Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
E [auth C]	Beta-Casp	e9kvdC1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: Beta-Casp	ECOD (v295)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
G	Light Chain	IGKV2	Kappa	spike protein s1	SAbDab (2026-08-14)
F [auth E]	Heavy Chain	IGHV4	-	spike protein s1	SAbDab (2026-08-14)
D [auth F]	Light Chain	IGLV1	Lambda	spike protein s1	SAbDab (2026-08-14)
C [auth D]	Heavy Chain	IGHV4	-	spike protein s1	SAbDab (2026-08-14)
B	Light Chain	IGKV1	Kappa	spike protein s1	SAbDab (2026-08-14)
A	Heavy Chain	IGHV3	-	spike protein s1	SAbDab (2026-08-14)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
G	The light chain of 3G5	-	-	-
F [auth E]	The heavy chain of 3G5	-	-	-
E [auth C]	Spike protein S1	identical protein binding protein binding binding host cell surface binding host cell surface receptor binding	viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell virion attachment to host cell biological process involved in interspecies interaction between organisms receptor-mediated virion attachment to host cell adhesion of symbiont to host cell viral life cycle adhesion of symbiont to host biological process involved in interaction with host biological process involved in symbiotic interaction membrane organization cellular component organization membrane fusion viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell virion attachment to host cell biological process involved in interspecies interaction between organisms receptor-mediated virion attachment to host cell adhesion of symbiont to host cell viral life cycle adhesion of symbiont to host biological process involved in interaction with host biological process involved in symbiotic interaction membrane organization cellular component organization membrane fusion fusion of virus membrane with host plasma membrane cellular process cellular component organization or biogenesis symbiont entry into host cell symbiont entry into host endocytosis involved in viral entry into host cell regulation of biological process positive regulation of viral life cycle positive regulation of viral process biological regulation positive regulation of biological process modulation by symbiont of entry into host regulation of viral entry into host cell regulation of viral life cycle regulation of viral process positive regulation of viral entry into host cell positive regulation by symbiont of entry into host regulation of biological process involved in symbiotic interaction	cellular anatomical structure membrane virion component virion membrane host intracellular membrane-bounded organelle host cellular component host intracellular part host cell membrane other organism part host cell cytoplasm part host intracellular organelle host cell endoplasmic reticulum-Golgi intermediate compartment membrane host cell endoplasmic reticulum-Golgi intermediate compartment host cell cytoplasm cellular anatomical structure membrane virion component virion membrane host intracellular membrane-bounded organelle host cellular component host intracellular part host cell membrane other organism part host cell cytoplasm part host intracellular organelle host cell endoplasmic reticulum-Golgi intermediate compartment membrane host cell endoplasmic reticulum-Golgi intermediate compartment host cell cytoplasm host cell part host intracellular region viral membrane viral envelope host cell plasma membrane
D [auth F]	The light chain of 4H5	-	-	-
C [auth D]	The heavy chain of 4H5	-	-	-
B	The light chain of 4C11	-	-	-
A	The heavy chain of 4C11	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E [auth C]	IPR018548	Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus	Domain
E [auth C]	IPR044341	Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like	Domain
E [auth C]	IPR032500	Spike glycoprotein S1, N-terminal domain, betacoronavirus-like	Domain
E [auth C]	IPR042578	Spike glycoprotein, betacoronavirus	Family
E [auth C]	IPR036326	Spike S1 subunit, receptor binding domain superfamily, betacoronavirus	Homologous Superfamily
E [auth C]	IPR043002	Spike glycoprotein, N-terminal domain superfamily	Homologous Superfamily
E [auth C]	IPR044874	Spike glycoprotein S2, coronavirus, heptad repeat 2	Domain
E [auth C]	IPR044873	Spike glycoprotein S2, coronavirus, heptad repeat 1	Domain
E [auth C]	IPR043473	Spike glycoprotein S2 superfamily, coronavirus	Homologous Superfamily
E [auth C]	IPR043607	Coronavirus spike glycoprotein S1, C-terminal	Domain
E [auth C]	IPR002552	Spike glycoprotein S2, coronavirus	Domain
E [auth C]	IPR044366	Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2	Domain

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

9KVD | pdb_00009kvd

Cryo-EM structure of SARS-CoV-2 prototype spike protein in complex with triple-nAb 3G5, 4H5 and 4C11

External Resource: Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

SAbDab Antibody Annotation SAbDab Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage