6VSJ

Cryo-electron microscopy structure of mouse coronavirus spike protein complexed with its murine receptor

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family 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	Coronavirus S1 glycoprotein domain D-like	8092669	3002616	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8091049	3000120	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Coronavirus S2 glycoprotein stalk-like	8091053	3000282	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Coronavirus S1 glycoprotein domain C-like	8092671	3002615	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	SARS coronavirus receptor-binding domain-like	8091051	3001706	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	SARS coronavirus receptor-binding domain-like	8091051	3001706	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8091049	3000120	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	Coronavirus S1 glycoprotein domain C-like	8092671	3002615	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	Coronavirus S1 glycoprotein domain D-like	8092669	3002616	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	Coronavirus S2 glycoprotein stalk-like	8091053	3000282	SCOP2B (2022-06-29)
E [auth C]	SCOP2B Superfamily	SARS coronavirus receptor-binding domain-like	8091051	3001706	SCOP2B (2022-06-29)
E [auth C]	SCOP2B Superfamily	Coronavirus S1 glycoprotein domain D-like	8092669	3002616	SCOP2B (2022-06-29)
E [auth C]	SCOP2B Superfamily	Coronavirus S2 glycoprotein stalk-like	8091053	3000282	SCOP2B (2022-06-29)
E [auth C]	SCOP2B Superfamily	Coronavirus S1 glycoprotein domain C-like	8092671	3002615	SCOP2B (2022-06-29)
E [auth C]	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8091049	3000120	SCOP2B (2022-06-29)
B [auth D]	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8094244	3000071	SCOP2B (2022-06-29)
D [auth E]	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8094244	3000071	SCOP2B (2022-06-29)
F	SCOP2 Family	V set domains-like	8094243	4007530	SCOP2 (2022-06-29)
F	SCOP2 Superfamily	Immunoglobulin (Ig) domain-like	8094244	3000071	SCOP2 (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	e6vsjA2	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: PF16451	ECOD (1.6)
A	PF19209	e6vsjA4	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	e6vsjA3	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	e6vsjA1	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)
C [auth B]	PF16451	e6vsjB2	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: PF16451	ECOD (1.6)
C [auth B]	PF19209	e6vsjB4	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)
C [auth B]	PF09408	e6vsjB3	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)
C [auth B]	PF01601	e6vsjB1	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)
E [auth C]	PF16451	e6vsjC2	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: PF16451	ECOD (1.6)
E [auth C]	PF19209	e6vsjC4	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 C]	PF09408	e6vsjC3	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)
E [auth C]	PF01601	e6vsjC1	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 D]	PF07686	e6vsjD1	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 E]	PF07686	e6vsjE1	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	PF07686	e6vsjF1	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)
B [auth D]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
D [auth E]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
F	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C [auth B], E [auth C]	PF01601	Coronavirus spike glycoprotein S2 (CoV_S2)	Coronavirus spike glycoprotein S2	-	Family
A, C [auth B], E [auth C]	PF16451	Betacoronavirus-like spike glycoprotein S1, N-terminal (bCoV_S1_N)	Betacoronavirus-like spike glycoprotein S1, N-terminal	This entry represents the N-terminal domain of the betacoronavirus-like trimeric spike glycoprotein. The distal S1 subunit of the coronavirus spike protein is responsible for receptor binding. S1 contains two domains; an N-terminal galectin-like doma ...	This entry represents the N-terminal domain of the betacoronavirus-like trimeric spike glycoprotein. The distal S1 subunit of the coronavirus spike protein is responsible for receptor binding. S1 contains two domains; an N-terminal galectin-like domain (NTD) and a receptor-binding domain (S1 RBD) also referred to as the S1 CTD or domain B. Either the S1 NTD or S1 RBD, or occasionally both, are involved in binding to host receptors. S1 NTD is located on the side of the spike trimer and mainly recognises sugar receptors [2]. For many betacoronaviruses (b-CoVs), for example mouse hepatitis virus (MHV), the RBD is located in the NTD. The structure of the MHV S1 NTD showed the same fold as human galectins (galactose-binding lectin), however it does not bind any sugar; instead, it binds to the carcinoembryonic antigen cell-adhesion molecule CEACAM1) through protein-protein interactions [2]. All three CEACAM21a-binding sites in MHV spikes can be fully occupied by CEACAM1a. It has been shown that CEACAM1a binding to the MHV spike weakens the interactions between S1 and S2 and facilitates the proteolysis of the spike protein and dissociation of S1 [2]. The homologous bovine CoV (BCov) S1 NTD also possesses a galectin fold but binds to sialic acid-containing moieties on host cell membranes, as does the NTD of three other group A b-Covs, namely human CoV (HCoV) OC43, avian b-CoV, and infectious bronchitis virus (IBV) [3]. Despite the S1 NTD of human respiratory b-CoV HKU1 being highly homologous to the NTDs of MHV and bovine CoV, it does not bind to either sugar or human carcinoembryonic antigen-related cell adhesion molecules (CEACAMs) and the RBD is found instead in the S1 RBD domain [3].	Domain
A, C [auth B], E [auth C]	PF09408	Betacoronavirus spike glycoprotein S1, receptor binding (bCoV_S1_RBD)	Betacoronavirus spike glycoprotein S1, receptor binding	This entry represents the receptor binding domain (S1 RBD) of the betacoronavirus spike glycoprotein. The spike glycoprotein is arranged in trimers on the surface of the viral membrane and is essential for viral entry. The spike protein is transla ...	This entry represents the receptor binding domain (S1 RBD) of the betacoronavirus spike glycoprotein. The spike glycoprotein is arranged in trimers on the surface of the viral membrane and is essential for viral entry. The spike protein is translated as a large polypeptide that is subsequently cleaved to the distal S1, responsible for receptor binding, and the membrane-anchored S2 responsible for membrane fusion [1]. The coronavirus (SARS-CoV) S1 subunit is composed of two distinct domains: an N-terminal domain (S1 NTD) and a receptor-binding domain (S1 RBD) also referred to as the S1 CTD or domain B. Each of these domains have been implicated in binding to host receptors. However, most coronaviruses are not known to utilise both the S1 NTD and S1 RBD for viral entry [2]. SARS-CoV makes use of its S1 RBD to bind to the human angiotensin-converting enzyme 2 (ACE2) as its host receptor [3,4].	Domain
A, C [auth B], E [auth C]	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
B [auth D], D [auth E], F	PF07686	Immunoglobulin V-set domain (V-set)	Immunoglobulin V-set domain	This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C [auth B], E [auth C]	Spike glycoprotein	identical protein binding protein binding 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 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	membrane cellular anatomical entity virion component virion membrane host cellular component host intracellular part host cell cytoplasm host cell part host cell Golgi apparatus host intracellular region host cell cytoplasm part host intracellular membrane-bounded organelle host cell membrane host intracellular organelle membrane cellular anatomical entity virion component virion membrane host cellular component host intracellular part host cell cytoplasm host cell part host cell Golgi apparatus host intracellular region host cell cytoplasm part host intracellular membrane-bounded organelle host cell membrane host intracellular organelle host cell endoplasmic reticulum-Golgi intermediate compartment membrane host cell endoplasmic reticulum-Golgi intermediate compartment viral membrane viral envelope host cell plasma membrane
B [auth D], D [auth E], F	Carcinoembryonic antigen-related cell adhesion molecule 1	-	-	membrane cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C [auth B], E [auth C]	IPR018548	Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus	Domain
A, C [auth B], E [auth C]	IPR032500	Spike glycoprotein S1, N-terminal domain, betacoronavirus-like	Domain
A, C [auth B], E [auth C]	IPR042578	Spike glycoprotein, betacoronavirus	Family
A, C [auth B], E [auth C]	IPR036326	Spike S1 subunit, receptor binding domain superfamily, betacoronavirus	Homologous Superfamily
A, C [auth B], E [auth C]	IPR043002	Spike glycoprotein, N-terminal domain superfamily	Homologous Superfamily
A, C [auth B], E [auth C]	IPR044339	Spike (S) protein S1 subunit, N-terminal domain, murine hepatitis virus-like	Domain
A, C [auth B], E [auth C]	IPR044874	Spike glycoprotein S2, coronavirus, heptad repeat 2	Domain
A, C [auth B], E [auth C]	IPR043614	Spike glycoprotein S2, coronavirus, C-terminal	Domain
A, C [auth B], E [auth C]	IPR044873	Spike glycoprotein S2, coronavirus, heptad repeat 1	Domain
A, C [auth B], E [auth C]	IPR043473	Spike glycoprotein S2 superfamily, coronavirus	Homologous Superfamily
A, C [auth B], E [auth C]	IPR043607	Coronavirus spike glycoprotein S1, C-terminal	Domain
A, C [auth B], E [auth C]	IPR002552	Spike glycoprotein S2, coronavirus	Domain
B [auth D], D [auth E], F	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
B [auth D], D [auth E], F	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
B [auth D], D [auth E], F	IPR003599	Immunoglobulin subtype	Domain
B [auth D], D [auth E], F	IPR003598	Immunoglobulin subtype 2	Domain
B [auth D], D [auth E], F	IPR013106	Immunoglobulin V-set domain	Domain
B [auth D], D [auth E], F	IPR007110	Immunoglobulin-like domain	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.