3BGF

X-ray crystal structure of the SARS coronavirus spike receptor binding domain in complex with F26G19 Fab

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A [auth S]	d3bgfs_	Alpha and beta proteins (a+b)	SARS receptor-binding domain-like	SARS receptor-binding domain-like	SARS receptor-binding domain-like	Spike protein S1	SARS-CoV (Severe acute respiratory syndrome-related coronavirus ) [TaxId: 694009 ],	SCOPe (2.08)
B [auth A]	d3bgfa_	Alpha and beta proteins (a+b)	SARS receptor-binding domain-like	SARS receptor-binding domain-like	SARS receptor-binding domain-like	Spike protein S1	SARS-CoV (Severe acute respiratory syndrome-related coronavirus ) [TaxId: 694009 ],	SCOPe (2.08)
C [auth L]	d3bgfl2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C [auth L]	d3bgfl1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
E [auth C]	d3bgfc2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
E [auth C]	d3bgfc1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
D [auth H]	d3bgfh_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
F [auth B]	d3bgfb_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth S]	SCOP2B Superfamily	SARS coronavirus receptor-binding domain-like	8041894	3001706	SCOP2B (2022-06-29)
B [auth A]	SCOP2B Superfamily	SARS coronavirus receptor-binding domain-like	8041894	3001706	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 [auth S]	Spike_rec_bind	e3bgfS1	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)
B [auth A]	Spike_rec_bind	e3bgfA1	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)
C [auth L]	C1-set_4	e3bgfL2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
C [auth L]	V-set	e3bgfL1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
E [auth C]	C1-set_4	e3bgfC2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
E [auth C]	V-set	e3bgfC1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
D [auth H]	V-set_8	e3bgfH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
D [auth H]	C1-set_1	e3bgfH2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
F [auth B]	V-set_8	e3bgfB1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
F [auth B]	C1-set_1	e3bgfB2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth S]	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 [auth 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)
C [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
E [auth C]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
F [auth B]	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 [auth L], E [auth C]	Fab F26G19	L-KAPPA	Mus musculus (house mouse)	IGKV9-12401, IGKJ101, IGKJ102, IGKC01, IGKC*02	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-2C_KAPPA	IMGT (202445-0)
D [auth H], F [auth B]	Fab F26G19	VH-CH1	Mus musculus (house mouse)	IGHV1-501, IGHJ401, IGHG2A01, IGHG2A02	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-2C_KAPPA	IMGT (202445-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
C [auth L], E [auth C]	Light Chain	IGKV9	Kappa	spike protein s1	SAbDab (2024-11-15)
D [auth H], F [auth B]	Heavy Chain	IGHV1	-	spike protein s1	SAbDab (2024-11-15)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth S], B [auth A]	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
C [auth L], E [auth C]	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
C [auth L], E [auth C]	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain	-	Domain
D [auth H], F [auth B]	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 [auth S], B [auth A]	Spike protein S1	host cell surface binding binding host cell surface receptor binding identical protein binding protein binding	viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell membrane organization cellular component organization membrane fusion cellular process cellular component organization or biogenesis symbiont-mediated perturbation of host defense response suppression by virus of host tetherin activity biological process involved in interspecies interaction between organisms modulation by virus of host process virus-mediated perturbation of host defense response biological process involved in interaction with host viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell membrane organization cellular component organization membrane fusion cellular process cellular component organization or biogenesis symbiont-mediated perturbation of host defense response suppression by virus of host tetherin activity biological process involved in interspecies interaction between organisms modulation by virus of host process virus-mediated perturbation of host defense response biological process involved in interaction with host biological process involved in symbiotic interaction symbiont-mediated perturbation of host process modulation of process of another organism modulation by virus of host cellular process virion attachment to host cell receptor-mediated virion attachment to host cell adhesion of symbiont to host cell viral life cycle adhesion of symbiont to host fusion of virus membrane with host plasma membrane 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 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 response to host defenses response to stimulus response to other organism symbiont-mediated perturbation of host immune response symbiont-mediated perturbation of host defenses response to defenses of other organism response to external stimulus response to biotic stimulus symbiont-mediated suppression of host immune response symbiont-mediated suppression of host innate immune response symbiont-mediated suppression of host defenses symbiont-mediated perturbation of host innate immune response response to host response to external biotic stimulus	cellular anatomical structure 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 host cell plasma membrane cellular anatomical structure 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 host cell plasma membrane virion component virion membrane viral membrane viral envelope
C [auth L], E [auth C]	F26G19 Fab	-	response to stimulus immune response immune system process	cellular anatomical structure extracellular region extracellular space
D [auth H], F [auth B]	F26G19 Fab	-	response to stimulus immune response immune system process adaptive immune response	protein-containing complex immunoglobulin complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth S], B [auth A]	IPR044873	Spike glycoprotein S2, coronavirus, heptad repeat 1	Domain
A [auth S], B [auth A]	IPR018548	Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus	Domain
A [auth S], B [auth A]	IPR044341	Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like	Domain
A [auth S], B [auth A]	IPR032500	Spike glycoprotein S1, N-terminal domain, betacoronavirus-like	Domain
A [auth S], B [auth A]	IPR042578	Spike glycoprotein, betacoronavirus	Family
A [auth S], B [auth A]	IPR036326	Spike S1 subunit, receptor binding domain superfamily, betacoronavirus	Homologous Superfamily
A [auth S], B [auth A]	IPR043002	Spike glycoprotein, N-terminal domain superfamily	Homologous Superfamily
A [auth S], B [auth A]	IPR044874	Spike glycoprotein S2, coronavirus, heptad repeat 2	Domain
A [auth S], B [auth A]	IPR043473	Spike glycoprotein S2 superfamily, coronavirus	Homologous Superfamily
A [auth S], B [auth A]	IPR002552	Spike glycoprotein S2, coronavirus	Domain
A [auth S], B [auth A]	IPR044370	Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV	Domain
C [auth L], E [auth C]	IPR003597	Immunoglobulin C1-set	Domain
C [auth L], E [auth C]	IPR050150	Immunoglobulin Variable Light Chain	Family
C [auth L], E [auth C]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
C [auth L], E [auth C]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
C [auth L], E [auth C]	IPR013106	Immunoglobulin V-set domain	Domain
C [auth L], E [auth C]	IPR003599	Immunoglobulin domain subtype	Domain
C [auth L], E [auth C]	IPR007110	Immunoglobulin-like domain	Domain
C [auth L], E [auth C]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
D [auth H], F [auth B]	IPR050199	Immunoglobulin Heavy Variable	Family
D [auth H], F [auth B]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
D [auth H], F [auth B]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
D [auth H], F [auth B]	IPR013106	Immunoglobulin V-set domain	Domain
D [auth H], F [auth B]	IPR003599	Immunoglobulin domain subtype	Domain
D [auth H], F [auth B]	IPR007110	Immunoglobulin-like domain	Domain