7OAY

Nanobody F2 bound to RBD

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 [auth AAA]	SCOP2B Superfamily	SARS coronavirus receptor-binding domain-like	8092467	3001706	SCOP2B (2022-06-29)
C [auth CCC]	SCOP2B Superfamily	SARS coronavirus receptor-binding domain-like	8092467	3001706	SCOP2B (2022-06-29)
E [auth EEE]	SCOP2B Superfamily	SARS coronavirus receptor-binding domain-like	8092467	3001706	SCOP2B (2022-06-29)
G [auth GGG]	SCOP2B Superfamily	SARS coronavirus receptor-binding domain-like	8092467	3001706	SCOP2B (2022-06-29)
I [auth III]	SCOP2B Superfamily	SARS coronavirus receptor-binding domain-like	8092467	3001706	SCOP2B (2022-06-29)
K [auth KKK]	SCOP2B Superfamily	SARS coronavirus receptor-binding domain-like	8092467	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 AAA]	Spike_rec_bind	e7oayAAA1	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 CCC]	Spike_rec_bind	e7oayCCC1	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)
E [auth EEE]	Spike_rec_bind	e7oayEEE1	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)
G [auth GGG]	Spike_rec_bind	e7oayGGG1	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)
I [auth III]	Spike_rec_bind	e7oayIII1	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)
K [auth KKK]	Spike_rec_bind	e7oayKKK1	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 BBB]	V-set_12	e7oayBBB1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)
D [auth DDD]	V-set_12	e7oayDDD1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)
F [auth FFF]	V-set_12	e7oayFFF1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)
H [auth HHH]	V-set_12	e7oayHHH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)
J [auth JJJ]	V-set_12	e7oayJJJ1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)
L [auth LLL]	V-set_12	e7oayLLL1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth AAA], C [auth CCC], E [auth EEE], G [auth GGG], I [auth III], A [auth AAA], C [auth CCC], E [auth EEE], G [auth GGG], I [auth III], K [auth KKK]	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth AAA], C [auth CCC], E [auth EEE], G [auth GGG], I [auth III], A [auth AAA], C [auth CCC], E [auth EEE], G [auth GGG], I [auth III], K [auth KKK]	Spike protein S1	protein binding binding molecular function activator activity signaling receptor binding molecular function regulator activity signaling receptor regulator activity receptor ligand activity signaling receptor activator activity host cell surface binding host cell surface receptor binding structural constituent of virion structural molecule activity identical 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 viral gene expression viral translation 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 entry receptor-mediated virion attachment to host cell	cellular anatomical structure membrane host extracellular space host cellular component cell periphery plasma membrane host intracellular membrane-bounded organelle 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 cellular anatomical structure membrane host extracellular space host cellular component cell periphery plasma membrane host intracellular membrane-bounded organelle 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 host cell surface
B [auth BBB], D [auth DDD], F [auth FFF], H [auth HHH], J [auth JJJ], B [auth BBB], D [auth DDD], F [auth FFF], H [auth HHH], J [auth JJJ], L [auth LLL]	F2 nanobody	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth AAA], C [auth CCC], E [auth EEE], G [auth GGG], I [auth III], A [auth AAA], C [auth CCC], E [auth EEE], G [auth GGG], I [auth III], K [auth KKK]	IPR044873	Spike glycoprotein S2, coronavirus, heptad repeat 1	Domain
A [auth AAA], C [auth CCC], E [auth EEE], G [auth GGG], I [auth III], A [auth AAA], C [auth CCC], E [auth EEE], G [auth GGG], I [auth III], K [auth KKK]	IPR044366	Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2	Domain
A [auth AAA], C [auth CCC], E [auth EEE], G [auth GGG], I [auth III], A [auth AAA], C [auth CCC], E [auth EEE], G [auth GGG], I [auth III], K [auth KKK]	IPR018548	Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus	Domain
A [auth AAA], C [auth CCC], E [auth EEE], G [auth GGG], I [auth III], A [auth AAA], C [auth CCC], E [auth EEE], G [auth GGG], I [auth III], K [auth KKK]	IPR044341	Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like	Domain
A [auth AAA], C [auth CCC], E [auth EEE], G [auth GGG], I [auth III], A [auth AAA], C [auth CCC], E [auth EEE], G [auth GGG], I [auth III], K [auth KKK]	IPR032500	Spike glycoprotein S1, N-terminal domain, betacoronavirus-like	Domain
A [auth AAA], C [auth CCC], E [auth EEE], G [auth GGG], I [auth III], A [auth AAA], C [auth CCC], E [auth EEE], G [auth GGG], I [auth III], K [auth KKK]	IPR042578	Spike glycoprotein, betacoronavirus	Family
A [auth AAA], C [auth CCC], E [auth EEE], G [auth GGG], I [auth III], A [auth AAA], C [auth CCC], E [auth EEE], G [auth GGG], I [auth III], K [auth KKK]	IPR036326	Spike S1 subunit, receptor binding domain superfamily, betacoronavirus	Homologous Superfamily
A [auth AAA], C [auth CCC], E [auth EEE], G [auth GGG], I [auth III], A [auth AAA], C [auth CCC], E [auth EEE], G [auth GGG], I [auth III], K [auth KKK]	IPR043002	Spike glycoprotein, N-terminal domain superfamily	Homologous Superfamily
A [auth AAA], C [auth CCC], E [auth EEE], G [auth GGG], I [auth III], A [auth AAA], C [auth CCC], E [auth EEE], G [auth GGG], I [auth III], K [auth KKK]	IPR044874	Spike glycoprotein S2, coronavirus, heptad repeat 2	Domain
A [auth AAA], C [auth CCC], E [auth EEE], G [auth GGG], I [auth III], A [auth AAA], C [auth CCC], E [auth EEE], G [auth GGG], I [auth III], K [auth KKK]	IPR043473	Spike glycoprotein S2 superfamily, coronavirus	Homologous Superfamily
A [auth AAA], C [auth CCC], E [auth EEE], G [auth GGG], I [auth III], A [auth AAA], C [auth CCC], E [auth EEE], G [auth GGG], I [auth III], K [auth KKK]	IPR043607	Coronavirus spike glycoprotein S1, C-terminal	Domain
A [auth AAA], C [auth CCC], E [auth EEE], G [auth GGG], I [auth III], A [auth AAA], C [auth CCC], E [auth EEE], G [auth GGG], I [auth III], K [auth KKK]	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.