5W9H | pdb_00005w9h

MERS S ectodomain trimer in complex with variable domain of neutralizing antibody G4

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody Annotation
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 S2 glycoprotein stalk-like	8092154	3000282	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Coronavirus spike S2 glycoprotein connector domain-like	8092156	3002562	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Coronavirus spike S2 glycoprotein connector domain-like	8092156	3002562	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Coronavirus S2 glycoprotein stalk-like	8092154	3000282	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Coronavirus S2 glycoprotein stalk-like	8092154	3000282	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Coronavirus spike S2 glycoprotein connector domain-like	8092156	3002562	SCOP2B (2022-06-29)
J [auth p]	SCOP2B Superfamily	Coronavirus S1 glycoprotein, domain C-like	8092665	3002615	SCOP2B (2022-06-29)
J [auth p]	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8092152	3000120	SCOP2B (2022-06-29)
J [auth p]	SCOP2B Superfamily	Coronavirus S1 glycoprotein, domain D-like	8092667	3002616	SCOP2B (2022-06-29)
J [auth p]	SCOP2B Superfamily	SARS coronavirus receptor-binding domain-like	8082394	3001706	SCOP2B (2022-06-29)
K [auth q]	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8092152	3000120	SCOP2B (2022-06-29)
K [auth q]	SCOP2B Superfamily	Coronavirus S1 glycoprotein, domain C-like	8092665	3002615	SCOP2B (2022-06-29)
K [auth q]	SCOP2B Superfamily	SARS coronavirus receptor-binding domain-like	8082394	3001706	SCOP2B (2022-06-29)
K [auth q]	SCOP2B Superfamily	Coronavirus S1 glycoprotein, domain D-like	8092667	3002616	SCOP2B (2022-06-29)
L [auth r]	SCOP2B Superfamily	SARS coronavirus receptor-binding domain-like	8082394	3001706	SCOP2B (2022-06-29)
L [auth r]	SCOP2B Superfamily	Coronavirus S1 glycoprotein, domain D-like	8092667	3002616	SCOP2B (2022-06-29)
L [auth r]	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8092152	3000120	SCOP2B (2022-06-29)
L [auth r]	SCOP2B Superfamily	Coronavirus S1 glycoprotein, domain C-like	8092665	3002615	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)
C	KOW5_SPT5	e5w9hC1	A: alpha bundles	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: KOW5_SPT5	ECOD (develop294)
F	KOW5_SPT5	e5w9hF1	A: alpha bundles	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: KOW5_SPT5	ECOD (develop294)
I	KOW5_SPT5	e5w9hI1	A: alpha bundles	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: KOW5_SPT5	ECOD (develop294)
B	KOW5_SPT5	e5w9hB1	A: alpha bundles	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: KOW5_SPT5	ECOD (develop294)
H	KOW5_SPT5	e5w9hH1	A: alpha bundles	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: KOW5_SPT5	ECOD (develop294)
E	KOW5_SPT5	e5w9hE1	A: alpha bundles	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: KOW5_SPT5	ECOD (develop294)
A	PDZ	e5w9hA1	A: alpha bundles	X: RING/U-box-like	H: UDP-Glycosyltransferase/glycogen phosphorylase	T: UDP-Glycosyltransferase/glycogen phosphorylase	F: PDZ	ECOD (develop294)
D	CoV_S2	e5w9hD1	A: alpha bundles	X: Family A G protein-coupled receptor-like	H: Sodium/proton antiporter subunits-like	T: NADH-quinone oxidoreductase subunit 8 (Nqo8)-related	F: CoV_S2	ECOD (develop294)
G	CoV_S2	e5w9hG1	A: alpha bundles	X: Family A G protein-coupled receptor-like	H: Sodium/proton antiporter subunits-like	T: NADH-quinone oxidoreductase subunit 8 (Nqo8)-related	F: CoV_S2	ECOD (develop294)
J [auth p]	KOW5_SPT5	e5w9hp1	A: alpha bundles	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: KOW5_SPT5	ECOD (develop294)
J [auth p]	B_lactamase-like_C	e5w9hp2	A: alpha bundles	X: P-loop domains-like	H: Hemagglutinin HA2 chain	T: Hemagglutinin HA2 chain	F: B_lactamase-like_C	ECOD (develop294)
K [auth q]	KOW5_SPT5	e5w9hq1	A: alpha bundles	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: KOW5_SPT5	ECOD (develop294)
K [auth q]	B_lactamase-like_C	e5w9hq2	A: alpha bundles	X: P-loop domains-like	H: Hemagglutinin HA2 chain	T: Hemagglutinin HA2 chain	F: B_lactamase-like_C	ECOD (develop294)
L [auth r]	KOW5_SPT5	e5w9hr1	A: alpha bundles	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: KOW5_SPT5	ECOD (develop294)
L [auth r]	B_lactamase-like_C	e5w9hr2	A: alpha bundles	X: P-loop domains-like	H: Hemagglutinin HA2 chain	T: Hemagglutinin HA2 chain	F: B_lactamase-like_C	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
F	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
I	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, F, I	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 (202610-0)
B, E, H	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 (202610-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
C, F, I	Light Chain	IGKV3	Kappa	mers s	SAbDab (2026-03-20)
B, E, H	Heavy Chain	IGHV1	-	mers s	SAbDab (2026-03-20)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, D, G, J [auth p], K [auth q], A, D, G, J [auth p], K [auth q], L [auth r]	PF01601	Coronavirus spike glycoprotein S2 (CoV_S2)	Coronavirus spike glycoprotein S2	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, F, I	G4 VL	-	-	-
B, E, H	G4 VH	-	-	-
A, D, G, J [auth p], K [auth q], A, D, G, J [auth p], K [auth q], L [auth r]	MERS S	-	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 symbiont entry into host cell symbiont entry into host endocytosis involved in viral entry into host cell 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	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, D, G, J [auth p], K [auth q], A, D, G, J [auth p], K [auth q], L [auth r]	IPR018548	Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus	Domain
A, D, G, J [auth p], K [auth q], A, D, G, J [auth p], K [auth q], L [auth r]	IPR032500	Spike glycoprotein S1, N-terminal domain, betacoronavirus-like	Domain
A, D, G, J [auth p], K [auth q], A, D, G, J [auth p], K [auth q], L [auth r]	IPR044376	Spike (S) protein S1 subunit, receptor-binding domain, MERS-CoV	Domain
A, D, G, J [auth p], K [auth q], A, D, G, J [auth p], K [auth q], L [auth r]	IPR042578	Spike glycoprotein, betacoronavirus	Family
A, D, G, J [auth p], K [auth q], A, D, G, J [auth p], K [auth q], L [auth r]	IPR036326	Spike S1 subunit, receptor binding domain superfamily, betacoronavirus	Homologous Superfamily
A, D, G, J [auth p], K [auth q], A, D, G, J [auth p], K [auth q], L [auth r]	IPR043002	Spike glycoprotein, N-terminal domain superfamily	Homologous Superfamily
A, D, G, J [auth p], K [auth q], A, D, G, J [auth p], K [auth q], L [auth r]	IPR044874	Spike glycoprotein S2, coronavirus, heptad repeat 2	Domain
A, D, G, J [auth p], K [auth q], A, D, G, J [auth p], K [auth q], L [auth r]	IPR044337	Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-like	Domain
A, D, G, J [auth p], K [auth q], A, D, G, J [auth p], K [auth q], L [auth r]	IPR043614	Spike glycoprotein S2, coronavirus, C-terminal	Domain
A, D, G, J [auth p], K [auth q], A, D, G, J [auth p], K [auth q], L [auth r]	IPR044873	Spike glycoprotein S2, coronavirus, heptad repeat 1	Domain
A, D, G, J [auth p], K [auth q], A, D, G, J [auth p], K [auth q], L [auth r]	IPR043473	Spike glycoprotein S2 superfamily, coronavirus	Homologous Superfamily
A, D, G, J [auth p], K [auth q], A, D, G, J [auth p], K [auth q], L [auth r]	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.