5SZS

Glycan shield and epitope masking of a coronavirus spike protein observed by cryo-electron microscopy

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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 C-like	8092697	3002615	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	SARS coronavirus receptor-binding domain-like	8053550	3001706	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8092695	3000120	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Coronavirus S1 glycoprotein, domain D-like	8092699	3002616	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Coronavirus S2 glycoprotein stalk-like	8092701	3000282	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Coronavirus spike S2 glycoprotein connector domain-like	8092703	3002562	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8092693	3000120	SCOP2B (2022-06-29)
B	SCOP2 Family	HCov-NL63 receptor-binding domain-like	8049253	4006418	SCOP2 (2022-06-29)
B	SCOP2 Family	Coronavirus spike S1 glycoprotein N-terminal domain-like	8092692	4004563	SCOP2 (2022-06-29)
B	SCOP2 Family	Coronavirus spike S1 glycoprotein N-terminal domain-like	8092694	4004563	SCOP2 (2022-06-29)
B	SCOP2 Family	Coronavirus S1 glycoprotein, domain C-like	8092696	4007778	SCOP2 (2022-06-29)
B	SCOP2 Family	Coronavirus S1 glycoprotein, domain D-like	8092698	4007779	SCOP2 (2022-06-29)
B	SCOP2 Family	Coronavirus S2 glycoprotein stalk-like	8092700	4003119	SCOP2 (2022-06-29)
B	SCOP2 Family	Coronavirus spike S2 glycoprotein connector domain-like	8092702	4007763	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	SARS coronavirus receptor-binding domain-like	8053550	3001706	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Concanavalin A-like lectins/glucanases	8092693	3000120	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Concanavalin A-like lectins/glucanases	8092695	3000120	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Coronavirus S1 glycoprotein, domain C-like	8092697	3002615	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Coronavirus S1 glycoprotein, domain D-like	8092699	3002616	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Coronavirus S2 glycoprotein stalk-like	8092701	3000282	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Coronavirus spike S2 glycoprotein connector domain-like	8092703	3002562	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	Coronavirus S1 glycoprotein, domain D-like	8092699	3002616	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8092693	3000120	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Coronavirus S1 glycoprotein, domain C-like	8092697	3002615	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Coronavirus spike S2 glycoprotein connector domain-like	8092703	3002562	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Coronavirus S2 glycoprotein stalk-like	8092701	3000282	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	SARS coronavirus receptor-binding domain-like	8053550	3001706	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8092695	3000120	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	Corona_S1_1st	e5szsA2	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: Corona_S1_1st	ECOD (1.6)
A	EUF07639	e5szsA1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: EUF07639	ECOD (1.6)
A	Corona_S1_3rd	e5szsA4	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: Corona_S1_3rd	ECOD (1.6)
A	Corona_S1_2nd	e5szsA3	A: a+b three layers	X: Coronavirus spike protein receptor-binding domain (From Homology)	H: Coronavirus spike protein receptor-binding domain	T: Alpha-coronavirus spike protein receptor-binding domain	F: Corona_S1_2nd	ECOD (1.6)
A	Corona_S2	e5szsA5	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: Corona_S2	ECOD (1.6)
B	Corona_S1_1st	e5szsB1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: Corona_S1_1st	ECOD (1.6)
B	EUF07639	e5szsB5	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: EUF07639	ECOD (1.6)
B	Corona_S1_3rd	e5szsB2	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: Corona_S1_3rd	ECOD (1.6)
B	Corona_S1_2nd	e5szsB3	A: a+b three layers	X: Coronavirus spike protein receptor-binding domain (From Homology)	H: Coronavirus spike protein receptor-binding domain	T: Alpha-coronavirus spike protein receptor-binding domain	F: Corona_S1_2nd	ECOD (1.6)
B	Corona_S2	e5szsB4	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: Corona_S2	ECOD (1.6)
C	Corona_S1_1st	e5szsC1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: Corona_S1_1st	ECOD (1.6)
C	EUF07639	e5szsC3	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: EUF07639	ECOD (1.6)
C	Corona_S1_3rd	e5szsC4	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: Corona_S1_3rd	ECOD (1.6)
C	Corona_S1_2nd	e5szsC2	A: a+b three layers	X: Coronavirus spike protein receptor-binding domain (From Homology)	H: Coronavirus spike protein receptor-binding domain	T: Alpha-coronavirus spike protein receptor-binding domain	F: Corona_S1_2nd	ECOD (1.6)
C	Corona_S2	e5szsC5	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: Corona_S2	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF01601	Coronavirus spike glycoprotein S2 (CoV_S2)	Coronavirus spike glycoprotein S2	-	Family
A, B, C	PF01600	Coronavirus spike glycoprotein S1 (CoV_S1)	Coronavirus spike glycoprotein S1	-	Family
A, B, 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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	Spike glycoprotein	host cell surface binding 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 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	cellular anatomical structure membrane 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 cellular anatomical structure membrane 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR002551	Spike glycoprotein S1, coronavirus	Domain
A, B, C	IPR044874	Spike glycoprotein S2, coronavirus, heptad repeat 2	Domain
A, B, C	IPR043614	Spike glycoprotein S2, coronavirus, C-terminal	Domain
A, B, C	IPR044873	Spike glycoprotein S2, coronavirus, heptad repeat 1	Domain
A, B, C	IPR043473	Spike glycoprotein S2 superfamily, coronavirus	Homologous Superfamily
A, B, C	IPR042552	Spike glycoprotein, Alphacoronavirus	Family
A, B, C	IPR043607	Coronavirus spike glycoprotein S1, C-terminal	Domain
A, B, C	IPR002552	Spike glycoprotein S2, coronavirus	Domain