Annotations: 5W9P

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth J]	SCOP2B Superfamily	Coronavirus spike S2 glycoprotein connector domain-like	8092156	3002562	SCOP2B (2022-06-29)
A [auth J]	SCOP2B Superfamily	Coronavirus S2 glycoprotein stalk-like	8092154	3000282	SCOP2B (2022-06-29)
B [auth A]	SCOP2B Superfamily	Coronavirus S1 glycoprotein domain C-like	8092665	3002615	SCOP2B (2022-06-29)
B [auth A]	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8092152	3000120	SCOP2B (2022-06-29)
B [auth A]	SCOP2B Superfamily	Coronavirus S1 glycoprotein domain D-like	8092667	3002616	SCOP2B (2022-06-29)
E [auth B]	SCOP2B Superfamily	Coronavirus spike S2 glycoprotein connector domain-like	8092156	3002562	SCOP2B (2022-06-29)
E [auth B]	SCOP2B Superfamily	Coronavirus S2 glycoprotein stalk-like	8092154	3000282	SCOP2B (2022-06-29)
I [auth H]	SCOP2B Superfamily	Coronavirus spike S2 glycoprotein connector domain-like	8092156	3002562	SCOP2B (2022-06-29)
I [auth H]	SCOP2B Superfamily	Coronavirus S2 glycoprotein stalk-like	8092154	3000282	SCOP2B (2022-06-29)
J [auth I]	SCOP2B Superfamily	Coronavirus S1 glycoprotein domain C-like	8092665	3002615	SCOP2B (2022-06-29)
J [auth I]	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8092152	3000120	SCOP2B (2022-06-29)
J [auth I]	SCOP2B Superfamily	Coronavirus S1 glycoprotein domain D-like	8092667	3002616	SCOP2B (2022-06-29)
F [auth C]	SCOP2B Superfamily	Coronavirus S1 glycoprotein domain C-like	8092665	3002615	SCOP2B (2022-06-29)
F [auth C]	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8092152	3000120	SCOP2B (2022-06-29)
F [auth C]	SCOP2B Superfamily	Coronavirus S1 glycoprotein domain D-like	8092667	3002616	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 [auth J]	PF01601	e5w9pJ1	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 A]	PF16451	e5w9pA1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: PF16451	ECOD (1.6)
B [auth A]	PF19209	e5w9pA2	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)
E [auth B]	PF01601	e5w9pB1	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)
I [auth H]	PF01601	e5w9pH1	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)
J [auth I]	PF16451	e5w9pI1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: PF16451	ECOD (1.6)
J [auth I]	PF19209	e5w9pI2	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)
F [auth C]	PF16451	e5w9pC1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: PF16451	ECOD (1.6)
F [auth C]	PF19209	e5w9pC2	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 D]	PF07686	e5w9pD1	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)
K	PF07686	e5w9pK1	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 F]	PF07686	e5w9pF1	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)
D [auth G]	PF07686	e5w9pG1	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 E]	PF07686	e5w9pE1	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)
L	PF07686	e5w9pL1	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D [auth G]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
H [auth E]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
L	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

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
C [auth F], G [auth D], K	Fab G4 , neutralizing	VH-CH1	Mus musculus (house mouse)	IGHV1S13701, IGHJ401, IGHG1*02	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202417-0)
D [auth G], H [auth E], L	Fab G4 , neutralizing	L-KAPPA	Mus musculus (house mouse)	IGKV3-201, IGKJ101, IGKJ201, IGKC01, IGKC*02	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202417-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
C [auth F], G [auth D], K	Heavy Chain	IGHV1	-	spike glycoprotein	SAbDab (2024-05-03)
D [auth G], H [auth E], L	Light Chain	IGKV3	Kappa	spike glycoprotein	SAbDab (2024-05-03)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth J], B [auth A], E [auth B], F [auth C], I [auth H], A [auth J], B [auth A], E [auth B], F [auth C], I [auth H], J [auth I]	PF01601	Coronavirus spike glycoprotein S2 (CoV_S2)	Coronavirus spike glycoprotein S2	-	Family
A [auth J], B [auth A], E [auth B], F [auth C], I [auth H], A [auth J], B [auth A], E [auth B], F [auth C], I [auth H], J [auth I]	PF19209	Coronavirus spike glycoprotein S1, C-terminal (CoV_S1_C)	Coronavirus spike glycoprotein S1, C-terminal	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 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

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth J], B [auth A], E [auth B], F [auth C], I [auth H], A [auth J], B [auth A], E [auth B], F [auth C], I [auth H], J [auth I]	Spike glycoprotein	-	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 cellular process cellular component organization or biogenesis fusion of virus membrane with host plasma membrane import into cell transport establishment of localization vesicle-mediated transport localization symbiont entry into host cell symbiont entry into host endocytosis involved in viral entry into host cell endocytosis transport of virus 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	membrane cellular anatomical entity virion component virion membrane host intracellular membrane-bounded organelle host cellular component 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 membrane cellular anatomical entity virion component virion membrane host intracellular membrane-bounded organelle host cellular component 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 viral membrane viral envelope host cell plasma membrane
C [auth F], G [auth D], K	G4 VH	-	-	-
D [auth G], H [auth E], L	G4 VL	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth J], B [auth A], E [auth B], F [auth C], I [auth H], A [auth J], B [auth A], E [auth B], F [auth C], I [auth H], J [auth I]	IPR018548	Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus	Domain
A [auth J], B [auth A], E [auth B], F [auth C], I [auth H], A [auth J], B [auth A], E [auth B], F [auth C], I [auth H], J [auth I]	IPR032500	Spike glycoprotein S1, N-terminal domain, betacoronavirus-like	Domain
A [auth J], B [auth A], E [auth B], F [auth C], I [auth H], A [auth J], B [auth A], E [auth B], F [auth C], I [auth H], J [auth I]	IPR044376	Spike (S) protein S1 subunit, receptor-binding domain, MERS-CoV	Domain
A [auth J], B [auth A], E [auth B], F [auth C], I [auth H], A [auth J], B [auth A], E [auth B], F [auth C], I [auth H], J [auth I]	IPR042578	Spike glycoprotein, betacoronavirus	Family
A [auth J], B [auth A], E [auth B], F [auth C], I [auth H], A [auth J], B [auth A], E [auth B], F [auth C], I [auth H], J [auth I]	IPR036326	Spike S1 subunit, receptor binding domain superfamily, betacoronavirus	Homologous Superfamily
A [auth J], B [auth A], E [auth B], F [auth C], I [auth H], A [auth J], B [auth A], E [auth B], F [auth C], I [auth H], J [auth I]	IPR043002	Spike glycoprotein, N-terminal domain superfamily	Homologous Superfamily
A [auth J], B [auth A], E [auth B], F [auth C], I [auth H], A [auth J], B [auth A], E [auth B], F [auth C], I [auth H], J [auth I]	IPR044874	Spike glycoprotein S2, coronavirus, heptad repeat 2	Domain
A [auth J], B [auth A], E [auth B], F [auth C], I [auth H], A [auth J], B [auth A], E [auth B], F [auth C], I [auth H], J [auth I]	IPR044337	Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-like	Domain
A [auth J], B [auth A], E [auth B], F [auth C], I [auth H], A [auth J], B [auth A], E [auth B], F [auth C], I [auth H], J [auth I]	IPR043614	Spike glycoprotein S2, coronavirus, C-terminal	Domain
A [auth J], B [auth A], E [auth B], F [auth C], I [auth H], A [auth J], B [auth A], E [auth B], F [auth C], I [auth H], J [auth I]	IPR044873	Spike glycoprotein S2, coronavirus, heptad repeat 1	Domain
A [auth J], B [auth A], E [auth B], F [auth C], I [auth H], A [auth J], B [auth A], E [auth B], F [auth C], I [auth H], J [auth I]	IPR043473	Spike glycoprotein S2 superfamily, coronavirus	Homologous Superfamily
A [auth J], B [auth A], E [auth B], F [auth C], I [auth H], A [auth J], B [auth A], E [auth B], F [auth C], I [auth H], J [auth I]	IPR043607	Coronavirus spike glycoprotein S1, C-terminal	Domain
A [auth J], B [auth A], E [auth B], F [auth C], I [auth H], A [auth J], B [auth A], E [auth B], F [auth C], I [auth H], J [auth I]	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.