7JV2

SARS-CoV-2 spike in complex with the S2H13 neutralizing antibody Fab fragment (local refinement of the receptor-binding motif and Fab variable domains)

External Resource: Annotation

Domain Annotation: ECOD Classification
IMGT Antibody Annotation
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)
A [auth H]	V-set_10	e7jv2H1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_10	ECOD (1.6)
B [auth L]	V-set_3	e7jv2L1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_3	ECOD (1.6)

IMGT Antibody Annotation IMGT Database Homepage

Chain	Protein Name	Description	Organism Name	Gene Allele Name(s)	Domain Name(s)	Receptor Type	Receptor Description	Provenance Source
A [auth H]	Fab S2H13, anti-SARS-CoV-2, neutralizing	VH	Homo sapiens (human)	IGHV3-701, IGHV3-702, IGHV3-703, IGHV3-704, IGHV3-705, IGHJ401, IGHJ402, IGHJ403, IGHJ301, IGHJ501, IGHJ8*01	V-DOMAIN VH	IG	FV-HEAVY_LAMBDA	IMGT (202442-0)
B [auth L]	Fab S2H13, anti-SARS-CoV-2, neutralizing	V-LAMBDA	Homo sapiens (human)	IGLV7-4601, IGLJ201, IGLJ302, IGLJ101, IGLJ3*01	V-DOMAIN V-LAMBDA	IG	FV-HEAVY_LAMBDA	IMGT (202442-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A [auth H]	Heavy Chain	IGHV3	-	sars-cov-2 spike glycoprotein	SAbDab (2024-10-25)
B [auth L]	Light Chain	IGLV7	Lambda	sars-cov-2 spike glycoprotein	SAbDab (2024-10-25)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth H]	S2H13 Fab heavy chain	-	-	-
B [auth L]	S2H13 Fab light chain	-	-	-
C [auth A]	Spike glycoprotein	protein binding binding molecular function activator activity signaling receptor binding molecular function regulator activity signaling receptor regulator activity receptor ligand activity signaling receptor activator activity host cell surface binding host cell surface receptor binding structural constituent of virion structural molecule activity identical protein binding	viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell membrane organization cellular component organization membrane fusion cellular process cellular component organization or biogenesis import into cell receptor-mediated endocytosis of virus by host cell biological process involved in interspecies interaction between organisms transport viral life cycle establishment of localization viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell membrane organization cellular component organization membrane fusion cellular process cellular component organization or biogenesis import into cell receptor-mediated endocytosis of virus by host cell biological process involved in interspecies interaction between organisms transport viral life cycle establishment of localization biological process involved in interaction with host vesicle-mediated transport biological process involved in symbiotic interaction localization symbiont entry into host cell symbiont entry into host endocytosis involved in viral entry into host cell endocytosis receptor-mediated endocytosis transport of virus symbiont-mediated perturbation of host defense response suppression by virus of host tetherin activity response to host defenses response to stimulus response to other organism response to defenses of other organism modulation by virus of host process response to external stimulus virus-mediated perturbation of host defense response response to biotic stimulus symbiont-mediated perturbation of host process response to host response to external biotic stimulus modulation of process of another organism modulation by virus of host cellular process virion attachment to host cell receptor-mediated virion attachment to host cell adhesion of symbiont to host cell adhesion of symbiont to host viral gene expression viral translation fusion of virus membrane with host plasma membrane 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 symbiont-mediated perturbation of host immune response symbiont-mediated perturbation of host defenses symbiont-mediated suppression of host immune response symbiont-mediated suppression of host innate immune response response to host immune response symbiont-mediated suppression of host defenses symbiont-mediated perturbation of host innate immune response entry receptor-mediated virion attachment to host cell	membrane cellular anatomical entity host extracellular space host cellular component cell periphery plasma membrane host intracellular membrane-bounded organelle host intracellular part host cell membrane 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 membrane cellular anatomical entity host extracellular space host cellular component cell periphery plasma membrane host intracellular membrane-bounded organelle host intracellular part host cell membrane 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 host cell plasma membrane virion component virion membrane viral membrane viral envelope host cell surface

InterPro: Protein Family Classification InterPro Database Homepage

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

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.