5W9K | pdb_00005w9k

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

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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)
D	SCOP2B Superfamily	Coronavirus S2 glycoprotein stalk-like	8092154	3000282	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Coronavirus spike S2 glycoprotein connector domain-like	8092156	3002562	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	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8092152	3000120	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Coronavirus S1 glycoprotein, domain D-like	8092667	3002616	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Coronavirus S1 glycoprotein, domain C-like	8092665	3002615	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	SARS coronavirus receptor-binding domain-like	8082394	3001706	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Coronavirus S1 glycoprotein, domain D-like	8092667	3002616	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Coronavirus S1 glycoprotein, domain C-like	8092665	3002615	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	SARS coronavirus receptor-binding domain-like	8082394	3001706	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8092152	3000120	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Coronavirus S1 glycoprotein, domain C-like	8092665	3002615	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8092152	3000120	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	SARS coronavirus receptor-binding domain-like	8082394	3001706	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Coronavirus spike S2 glycoprotein connector domain-like	8092156	3002562	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Coronavirus S2 glycoprotein stalk-like	8092154	3000282	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	e5w9kC1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: KOW5_SPT5	ECOD (v294.1)
F	KOW5_SPT5	e5w9kF1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: KOW5_SPT5	ECOD (v294.1)
I	KOW5_SPT5	e5w9kI1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: KOW5_SPT5	ECOD (v294.1)
B	KOW5_SPT5	e5w9kB1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: KOW5_SPT5	ECOD (v294.1)
H	KOW5_SPT5	e5w9kH1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: KOW5_SPT5	ECOD (v294.1)
E	KOW5_SPT5	e5w9kE1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: KOW5_SPT5	ECOD (v294.1)
G	KOW5_SPT5	e5w9kG1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: KOW5_SPT5	ECOD (v294.1)
J	KOW5_SPT5	e5w9kJ1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: KOW5_SPT5	ECOD (v294.1)
J	B_lactamase-like_C	e5w9kJ2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Hemagglutinin HA2 chain	T: Hemagglutinin HA2 chain	F: B_lactamase-like_C	ECOD (v294.1)
K	KOW5_SPT5	e5w9kK1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: KOW5_SPT5	ECOD (v294.1)
K	B_lactamase-like_C	e5w9kK2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Hemagglutinin HA2 chain	T: Hemagglutinin HA2 chain	F: B_lactamase-like_C	ECOD (v294.1)
L	KOW5_SPT5	e5w9kL1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: KOW5_SPT5	ECOD (v294.1)
L	B_lactamase-like_C	e5w9kL2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Hemagglutinin HA2 chain	T: Hemagglutinin HA2 chain	F: B_lactamase-like_C	ECOD (v294.1)

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 (202611-0)
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 (202611-0)

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	spike glycoprotein	SAbDab (2026-03-27)
B, E, H	Heavy Chain	IGHV1	-	spike glycoprotein	SAbDab (2026-03-27)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, D, G, J, K A, D, G, J, K, L	PF01601	Coronavirus spike glycoprotein S2 (CoV_S2)	Coronavirus spike glycoprotein S2	-	Family
A, D, G, J, K A, D, G, J, K, L	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, D, G, J, K A, D, G, J, K, L	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 translat ...	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

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, K A, D, G, J, K, L	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 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, K A, D, G, J, K, L	IPR018548	Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus	Domain
A, D, G, J, K A, D, G, J, K, L	IPR032500	Spike glycoprotein S1, N-terminal domain, betacoronavirus-like	Domain
A, D, G, J, K A, D, G, J, K, L	IPR044376	Spike (S) protein S1 subunit, receptor-binding domain, MERS-CoV	Domain
A, D, G, J, K A, D, G, J, K, L	IPR042578	Spike glycoprotein, betacoronavirus	Family
A, D, G, J, K A, D, G, J, K, L	IPR036326	Spike S1 subunit, receptor binding domain superfamily, betacoronavirus	Homologous Superfamily
A, D, G, J, K A, D, G, J, K, L	IPR043002	Spike glycoprotein, N-terminal domain superfamily	Homologous Superfamily
A, D, G, J, K A, D, G, J, K, L	IPR044874	Spike glycoprotein S2, coronavirus, heptad repeat 2	Domain
A, D, G, J, K A, D, G, J, K, L	IPR044337	Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-like	Domain
A, D, G, J, K A, D, G, J, K, L	IPR043614	Spike glycoprotein S2, coronavirus, C-terminal	Domain
A, D, G, J, K A, D, G, J, K, L	IPR044873	Spike glycoprotein S2, coronavirus, heptad repeat 1	Domain
A, D, G, J, K A, D, G, J, K, L	IPR043473	Spike glycoprotein S2 superfamily, coronavirus	Homologous Superfamily
A, D, G, J, K A, D, G, J, K, L	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.