8J1V

Cryo-EM structure of SARS-CoV2 Omicron BA.5 spike in complex with 8-9D Fabs

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
SAbDab Antibody Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	SARS coronavirus receptor-binding domain-like	8092467	3001706	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Coronavirus S2 glycoprotein stalk-like	8092471	3000282	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Coronavirus S1 glycoprotein domain C-like	8092661	3002615	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8092469	3000120	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Coronavirus spike S2 glycoprotein connector domain-like	8092473	3002562	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	Coronavirus spike S2 glycoprotein connector domain-like	8092473	3002562	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	Coronavirus S2 glycoprotein stalk-like	8092471	3000282	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8092469	3000120	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	Coronavirus S1 glycoprotein domain C-like	8092661	3002615	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	SARS coronavirus receptor-binding domain-like	8092467	3001706	SCOP2B (2022-06-29)
G [auth E]	SCOP2B Superfamily	Coronavirus spike S2 glycoprotein connector domain-like	8092473	3002562	SCOP2B (2022-06-29)
G [auth E]	SCOP2B Superfamily	Coronavirus S1 glycoprotein domain C-like	8092661	3002615	SCOP2B (2022-06-29)
G [auth E]	SCOP2B Superfamily	Coronavirus S2 glycoprotein stalk-like	8092471	3000282	SCOP2B (2022-06-29)
G [auth E]	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8092469	3000120	SCOP2B (2022-06-29)
G [auth E]	SCOP2B Superfamily	SARS coronavirus receptor-binding domain-like	8092467	3001706	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PF16451	e8j1vA1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: PF16451	ECOD (1.6)
A	PF19209	e8j1vA3	A: beta complex topology	X: Beta domain of coronavirus spike glycoprotein (From Topology)	H: Beta domain of coronavirus spike glycoprotein (From Topology)	T: Beta domain of coronavirus spike glycoprotein	F: PF19209	ECOD (1.6)
A	PF09408	e8j1vA4	A: a+b three layers	X: Coronavirus spike protein receptor-binding domain (From Homology)	H: Coronavirus spike protein receptor-binding domain	T: Beta-coronavirus spike protein receptor-binding domain	F: PF09408	ECOD (1.6)
A	PF01601	e8j1vA2	A: a+b complex topology	X: S2 subunit of coronavirus spike glycoprotein (From Topology)	H: S2 subunit of coronavirus spike glycoprotein (From Topology)	T: S2 subunit of coronavirus spike glycoprotein	F: PF01601	ECOD (1.6)
D [auth B]	PF16451	e8j1vB4	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: PF16451	ECOD (1.6)
D [auth B]	PF19209	e8j1vB2	A: beta complex topology	X: Beta domain of coronavirus spike glycoprotein (From Topology)	H: Beta domain of coronavirus spike glycoprotein (From Topology)	T: Beta domain of coronavirus spike glycoprotein	F: PF19209	ECOD (1.6)
D [auth B]	PF09408	e8j1vB3	A: a+b three layers	X: Coronavirus spike protein receptor-binding domain (From Homology)	H: Coronavirus spike protein receptor-binding domain	T: Beta-coronavirus spike protein receptor-binding domain	F: PF09408	ECOD (1.6)
D [auth B]	PF01601	e8j1vB1	A: a+b complex topology	X: S2 subunit of coronavirus spike glycoprotein (From Topology)	H: S2 subunit of coronavirus spike glycoprotein (From Topology)	T: S2 subunit of coronavirus spike glycoprotein	F: PF01601	ECOD (1.6)
G [auth E]	PF16451	e8j1vE3	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: PF16451	ECOD (1.6)
G [auth E]	PF19209	e8j1vE2	A: beta complex topology	X: Beta domain of coronavirus spike glycoprotein (From Topology)	H: Beta domain of coronavirus spike glycoprotein (From Topology)	T: Beta domain of coronavirus spike glycoprotein	F: PF19209	ECOD (1.6)
G [auth E]	PF09408	e8j1vE4	A: a+b three layers	X: Coronavirus spike protein receptor-binding domain (From Homology)	H: Coronavirus spike protein receptor-binding domain	T: Beta-coronavirus spike protein receptor-binding domain	F: PF09408	ECOD (1.6)
G [auth E]	PF01601	e8j1vE1	A: a+b complex topology	X: S2 subunit of coronavirus spike glycoprotein (From Topology)	H: S2 subunit of coronavirus spike glycoprotein (From Topology)	T: S2 subunit of coronavirus spike glycoprotein	F: PF01601	ECOD (1.6)
B [auth H]	PF07686	e8j1vH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
E [auth C]	PF07686	e8j1vC1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
H [auth F]	PF07686	e8j1vF1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
C [auth K]	PF07686	e8j1vK1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
F [auth D]	PF07686	e8j1vD1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
I [auth G]	PF07686	e8j1vG1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B [auth H], E [auth C], H [auth F]	Heavy Chain	IGHV3	-	spike protein s2'	SAbDab (2024-05-10)
C [auth K], F [auth D], I [auth G]	Light Chain	IGKV1	Kappa	spike protein s2'	SAbDab (2024-05-10)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, D [auth B], G [auth E]	Spike protein S2'	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 modulation by symbiont 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 symbiont-mediated perturbation of host cellular process symbiont-mediated suppression of host type I interferon-mediated signaling pathway symbiont-mediated suppression of host signal transduction pathway symbiont-mediated suppression of host interferon-mediated signaling pathway symbiont-mediated perturbation of host signal transduction pathway 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 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
B [auth H], E [auth C], H [auth F]	8-9D heavy chain	-	-	-
C [auth K], F [auth D], I [auth G]	8-9D light chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, D [auth B], G [auth E]	IPR044873	Spike glycoprotein S2, coronavirus, heptad repeat 1	Domain
A, D [auth B], G [auth E]	IPR044366	Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2	Domain
A, D [auth B], G [auth E]	IPR018548	Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus	Domain
A, D [auth B], G [auth E]	IPR044341	Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like	Domain
A, D [auth B], G [auth E]	IPR032500	Spike glycoprotein S1, N-terminal domain, betacoronavirus-like	Domain
A, D [auth B], G [auth E]	IPR042578	Spike glycoprotein, betacoronavirus	Family
A, D [auth B], G [auth E]	IPR036326	Spike S1 subunit, receptor binding domain superfamily, betacoronavirus	Homologous Superfamily
A, D [auth B], G [auth E]	IPR043002	Spike glycoprotein, N-terminal domain superfamily	Homologous Superfamily
A, D [auth B], G [auth E]	IPR044874	Spike glycoprotein S2, coronavirus, heptad repeat 2	Domain
A, D [auth B], G [auth E]	IPR043473	Spike glycoprotein S2 superfamily, coronavirus	Homologous Superfamily
A, D [auth B], G [auth E]	IPR043607	Coronavirus spike glycoprotein S1, C-terminal	Domain
A, D [auth B], G [auth E]	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 R01GM133198.