4L3N | pdb_00004l3n

Crystal structure of the receptor-binding domain from newly emerged Middle East respiratory syndrome coronavirus

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
B	SCOP2B Superfamily	SARS coronavirus receptor-binding domain-like	8092522	3001706	SCOP2B (2022-06-29)
A	SCOP2 Family	SARS coronavirus receptor-binding domain-like	8092521	4003874	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	SARS coronavirus receptor-binding domain-like	8092522	3001706	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)
B	Spike_rec_bind	e4l3nB1	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: Spike_rec_bind	ECOD (1.6)
A	Spike_rec_bind	e4l3nA1	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: Spike_rec_bind	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.30.70.1840	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Spike protein, C-terminal core receptor binding subdomain	CATH (4.3.0)
B	2.20.210.30	Mainly Beta	Single Sheet	ubp-family deubiquitinating enzyme fold		CATH (4.3.0)
A	3.30.70.1840	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Spike protein, C-terminal core receptor binding subdomain	CATH (4.3.0)
A	2.20.210.30	Mainly Beta	Single Sheet	ubp-family deubiquitinating enzyme fold		CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	S protein	-	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 symbiont entry into host cell symbiont entry into host endocytosis involved in viral entry into host cell	cellular anatomical structure membrane virion component virion membrane host intracellular membrane-bounded organelle host cellular component host intracellular part host cell membrane other organism part 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 cellular anatomical structure membrane virion component virion membrane host intracellular membrane-bounded organelle host cellular component host intracellular part host cell membrane other organism part 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR018548	Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus	Domain
A, B	IPR032500	Spike glycoprotein S1, N-terminal domain, betacoronavirus-like	Domain
A, B	IPR044376	Spike (S) protein S1 subunit, receptor-binding domain, MERS-CoV	Domain
A, B	IPR042578	Spike glycoprotein, betacoronavirus	Family
A, B	IPR036326	Spike S1 subunit, receptor binding domain superfamily, betacoronavirus	Homologous Superfamily
A, B	IPR043002	Spike glycoprotein, N-terminal domain superfamily	Homologous Superfamily
A, B	IPR044874	Spike glycoprotein S2, coronavirus, heptad repeat 2	Domain
A, B	IPR044337	Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-like	Domain
A, B	IPR043614	Spike glycoprotein S2, coronavirus, C-terminal	Domain
A, B	IPR044873	Spike glycoprotein S2, coronavirus, heptad repeat 1	Domain
A, B	IPR043473	Spike glycoprotein S2 superfamily, coronavirus	Homologous Superfamily
A, B	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.