9NRX | pdb_00009nrx

Venezuelan Equine Encephalitis Virus in complex with the single domain antibody V2B3

External Resource: Annotation

Domain Annotation: ECOD Classification
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A [auth B]	DNA_ligase_A_N	e9nrxB1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: DNA_ligase_A_N	ECOD (v295.2)
B [auth G]	DNA_ligase_A_N	e9nrxG1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: DNA_ligase_A_N	ECOD (v295.2)
E [auth O]	DNA_ligase_A_N	e9nrxO1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: DNA_ligase_A_N	ECOD (v295.2)
J [auth b]	LSDAT_euk	e9nrxb1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: LSDAT_euk	ECOD (v295.2)
K [auth g]	DNA_ligase_A_N	e9nrxg1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: DNA_ligase_A_N	ECOD (v295.2)
N [auth o]	DNA_ligase_A_N	e9nrxo1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: DNA_ligase_A_N	ECOD (v295.2)
P [auth R]	DNA_ligase_A_N	e9nrxR1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: DNA_ligase_A_N	ECOD (v295.2)
Q [auth S]	DNA_ligase_A_N	e9nrxS1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: DNA_ligase_A_N	ECOD (v295.2)
T [auth V]	DNA_ligase_A_N	e9nrxV1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: DNA_ligase_A_N	ECOD (v295.2)
V [auth r]	DNA_ligase_A_N	e9nrxr1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: DNA_ligase_A_N	ECOD (v295.2)
W [auth s]	DNA_ligase_A_N	e9nrxs1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: DNA_ligase_A_N	ECOD (v295.2)
Z [auth v]	DNA_ligase_A_N	e9nrxv1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: DNA_ligase_A_N	ECOD (v295.2)
AA [auth w]	DNA_ligase_A_N	e9nrxw1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: DNA_ligase_A_N	ECOD (v295.2)
C [auth J]	DNA_ligase_A_N	e9nrxJ1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: DNA_ligase_A_N	ECOD (v295.2)
D [auth N]	DNA_ligase_A_N	e9nrxN1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: DNA_ligase_A_N	ECOD (v295.2)
F [auth Q]	DNA_ligase_A_N	e9nrxQ1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: DNA_ligase_A_N	ECOD (v295.2)
L [auth j]	LSDAT_euk	e9nrxj1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: LSDAT_euk	ECOD (v295.2)
M [auth n]	DNA_ligase_A_N	e9nrxn1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: DNA_ligase_A_N	ECOD (v295.2)
O [auth q]	DNA_ligase_A_N	e9nrxq1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: DNA_ligase_A_N	ECOD (v295.2)
R [auth T]	DNA_ligase_A_N	e9nrxT1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: DNA_ligase_A_N	ECOD (v295.2)
S [auth U]	DNA_ligase_A_N	e9nrxU1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: DNA_ligase_A_N	ECOD (v295.2)
U [auth W]	DNA_ligase_A_N	e9nrxW1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: DNA_ligase_A_N	ECOD (v295.2)
X [auth t]	DNA_ligase_A_N	e9nrxt1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: DNA_ligase_A_N	ECOD (v295.2)
Y [auth u]	DNA_ligase_A_N	e9nrxu1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: DNA_ligase_A_N	ECOD (v295.2)
G [auth X]	CPSase_L_D2	e9nrxX1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: CPSase_L_D2	ECOD (v295.2)
H [auth Y]	CPSase_L_D2	e9nrxY1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: CPSase_L_D2	ECOD (v295.2)
I [auth Z]	CPSase_L_D2	e9nrxZ1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: CPSase_L_D2	ECOD (v295.2)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth B], B [auth G], E [auth O], J [auth b], K [auth g], A [auth B], B [auth G], E [auth O], J [auth b], K [auth g], N [auth o], P [auth R], Q [auth S], T [auth V], V [auth r], W [auth s], Z [auth v]	E1 envelope glycoprotein	peptidase activity catalytic activity, acting on a protein serine hydrolase activity serine-type peptidase activity hydrolase activity serine-type endopeptidase activity catalytic activity endopeptidase activity RNA binding binding nucleic acid binding structural molecule activity	viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell symbiont-mediated perturbation of host cellular process symbiont-mediated suppression of host gene expression biological process involved in interspecies interaction between organisms symbiont-mediated perturbation of host process symbiont-mediated perturbation of host gene expression modulation of process of another organism biological process involved in interaction with host biological process involved in symbiotic interaction import into cell receptor-mediated endocytosis of virus by host cell transport viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell symbiont-mediated perturbation of host cellular process symbiont-mediated suppression of host gene expression biological process involved in interspecies interaction between organisms symbiont-mediated perturbation of host process symbiont-mediated perturbation of host gene expression modulation of process of another organism biological process involved in interaction with host biological process involved in symbiotic interaction import into cell receptor-mediated endocytosis of virus by host cell transport viral life cycle establishment of localization vesicle-mediated transport localization symbiont entry into host cell clathrin-dependent endocytosis symbiont entry into host cellular process clathrin-dependent endocytosis of virus by host cell receptor-mediated endocytosis endocytosis endocytosis involved in viral entry into host cell proteolysis metabolic process primary metabolic process protein metabolic process macromolecule metabolic process virion attachment to host cell receptor-mediated virion attachment to host cell adhesion of symbiont to host cell entry receptor-mediated virion attachment to host cell adhesion of symbiont to host	host cell plasma membrane host cellular component cellular anatomical structure host cell part host cell membrane other organism part host intracellular part host cell cytoplasm host intracellular region virion component virion membrane viral capsid icosahedral viral capsid T=4 icosahedral viral capsid host cell plasma membrane host cellular component cellular anatomical structure host cell part host cell membrane other organism part host intracellular part host cell cytoplasm host intracellular region virion component virion membrane viral capsid icosahedral viral capsid T=4 icosahedral viral capsid host intracellular membrane-bounded organelle host cell nucleus host intracellular organelle viral membrane viral envelope
AA [auth w], C [auth J], D [auth N], F [auth Q], L [auth j], AA [auth w], C [auth J], D [auth N], F [auth Q], L [auth j], M [auth n], O [auth q], R [auth T], S [auth U], U [auth W], X [auth t], Y [auth u]	E2 envelope glycoprotein	peptidase activity catalytic activity, acting on a protein serine hydrolase activity serine-type peptidase activity hydrolase activity serine-type endopeptidase activity catalytic activity endopeptidase activity RNA binding binding nucleic acid binding structural molecule activity	viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell symbiont-mediated perturbation of host cellular process symbiont-mediated suppression of host gene expression biological process involved in interspecies interaction between organisms symbiont-mediated perturbation of host process symbiont-mediated perturbation of host gene expression modulation of process of another organism biological process involved in interaction with host biological process involved in symbiotic interaction import into cell receptor-mediated endocytosis of virus by host cell transport viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell symbiont-mediated perturbation of host cellular process symbiont-mediated suppression of host gene expression biological process involved in interspecies interaction between organisms symbiont-mediated perturbation of host process symbiont-mediated perturbation of host gene expression modulation of process of another organism biological process involved in interaction with host biological process involved in symbiotic interaction import into cell receptor-mediated endocytosis of virus by host cell transport viral life cycle establishment of localization vesicle-mediated transport localization symbiont entry into host cell clathrin-dependent endocytosis symbiont entry into host cellular process clathrin-dependent endocytosis of virus by host cell receptor-mediated endocytosis endocytosis endocytosis involved in viral entry into host cell proteolysis metabolic process primary metabolic process protein metabolic process macromolecule metabolic process virion attachment to host cell receptor-mediated virion attachment to host cell adhesion of symbiont to host cell entry receptor-mediated virion attachment to host cell adhesion of symbiont to host	host cell plasma membrane host cellular component cellular anatomical structure host cell part host cell membrane other organism part host intracellular part host cell cytoplasm host intracellular region virion component virion membrane viral capsid icosahedral viral capsid T=4 icosahedral viral capsid host cell plasma membrane host cellular component cellular anatomical structure host cell part host cell membrane other organism part host intracellular part host cell cytoplasm host intracellular region virion component virion membrane viral capsid icosahedral viral capsid T=4 icosahedral viral capsid host intracellular membrane-bounded organelle host cell nucleus host intracellular organelle viral membrane viral envelope
G [auth X], H [auth Y], I [auth Z]	Single domain antibody (nanobody) V2B3	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth B], B [auth G], E [auth O], J [auth b], K [auth g], A [auth B], B [auth G], E [auth O], J [auth b], K [auth g], N [auth o], P [auth R], Q [auth S], T [auth V], V [auth r], W [auth s], Z [auth v]	IPR002533	Alphavirus E3 spike glycoprotein	Domain
A [auth B], B [auth G], E [auth O], J [auth b], K [auth g], A [auth B], B [auth G], E [auth O], J [auth b], K [auth g], N [auth o], P [auth R], Q [auth S], T [auth V], V [auth r], W [auth s], Z [auth v]	IPR038055	Flaviviral glycoprotein E, dimerisation domain	Homologous Superfamily
A [auth B], B [auth G], E [auth O], J [auth b], K [auth g], A [auth B], B [auth G], E [auth O], J [auth b], K [auth g], N [auth o], P [auth R], Q [auth S], T [auth V], V [auth r], W [auth s], Z [auth v]	IPR014756	Immunoglobulin E-set	Homologous Superfamily
A [auth B], B [auth G], E [auth O], J [auth b], K [auth g], A [auth B], B [auth G], E [auth O], J [auth b], K [auth g], N [auth o], P [auth R], Q [auth S], T [auth V], V [auth r], W [auth s], Z [auth v]	IPR042304	Alphavirus E2 glycoprotein, domain A	Homologous Superfamily
A [auth B], B [auth G], E [auth O], J [auth b], K [auth g], A [auth B], B [auth G], E [auth O], J [auth b], K [auth g], N [auth o], P [auth R], Q [auth S], T [auth V], V [auth r], W [auth s], Z [auth v]	IPR036253	Flavivirus glycoprotein, central and dimerisation domain superfamily	Homologous Superfamily
A [auth B], B [auth G], E [auth O], J [auth b], K [auth g], A [auth B], B [auth G], E [auth O], J [auth b], K [auth g], N [auth o], P [auth R], Q [auth S], T [auth V], V [auth r], W [auth s], Z [auth v]	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
A [auth B], B [auth G], E [auth O], J [auth b], K [auth g], A [auth B], B [auth G], E [auth O], J [auth b], K [auth g], N [auth o], P [auth R], Q [auth S], T [auth V], V [auth r], W [auth s], Z [auth v]	IPR042305	Alphavirus E2 glycoprotein, domain B	Homologous Superfamily
A [auth B], B [auth G], E [auth O], J [auth b], K [auth g], A [auth B], B [auth G], E [auth O], J [auth b], K [auth g], N [auth o], P [auth R], Q [auth S], T [auth V], V [auth r], W [auth s], Z [auth v]	IPR042306	Alphavirus E2 glycoprotein, domain C	Homologous Superfamily
A [auth B], B [auth G], E [auth O], J [auth b], K [auth g], A [auth B], B [auth G], E [auth O], J [auth b], K [auth g], N [auth o], P [auth R], Q [auth S], T [auth V], V [auth r], W [auth s], Z [auth v]	IPR000936	Alphavirus E2 glycoprotein	Family
A [auth B], B [auth G], E [auth O], J [auth b], K [auth g], A [auth B], B [auth G], E [auth O], J [auth b], K [auth g], N [auth o], P [auth R], Q [auth S], T [auth V], V [auth r], W [auth s], Z [auth v]	IPR000930	Peptidase S3, togavirin	Domain
A [auth B], B [auth G], E [auth O], J [auth b], K [auth g], A [auth B], B [auth G], E [auth O], J [auth b], K [auth g], N [auth o], P [auth R], Q [auth S], T [auth V], V [auth r], W [auth s], Z [auth v]	IPR002548	Alphavirus E1 glycoprotein	Domain
A [auth B], B [auth G], E [auth O], J [auth b], K [auth g], A [auth B], B [auth G], E [auth O], J [auth b], K [auth g], N [auth o], P [auth R], Q [auth S], T [auth V], V [auth r], W [auth s], Z [auth v]	IPR000336	Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily	Homologous Superfamily
AA [auth w], C [auth J], D [auth N], F [auth Q], L [auth j], AA [auth w], C [auth J], D [auth N], F [auth Q], L [auth j], M [auth n], O [auth q], R [auth T], S [auth U], U [auth W], X [auth t], Y [auth u]	IPR002533	Alphavirus E3 spike glycoprotein	Domain
AA [auth w], C [auth J], D [auth N], F [auth Q], L [auth j], AA [auth w], C [auth J], D [auth N], F [auth Q], L [auth j], M [auth n], O [auth q], R [auth T], S [auth U], U [auth W], X [auth t], Y [auth u]	IPR038055	Flaviviral glycoprotein E, dimerisation domain	Homologous Superfamily
AA [auth w], C [auth J], D [auth N], F [auth Q], L [auth j], AA [auth w], C [auth J], D [auth N], F [auth Q], L [auth j], M [auth n], O [auth q], R [auth T], S [auth U], U [auth W], X [auth t], Y [auth u]	IPR014756	Immunoglobulin E-set	Homologous Superfamily
AA [auth w], C [auth J], D [auth N], F [auth Q], L [auth j], AA [auth w], C [auth J], D [auth N], F [auth Q], L [auth j], M [auth n], O [auth q], R [auth T], S [auth U], U [auth W], X [auth t], Y [auth u]	IPR042304	Alphavirus E2 glycoprotein, domain A	Homologous Superfamily
AA [auth w], C [auth J], D [auth N], F [auth Q], L [auth j], AA [auth w], C [auth J], D [auth N], F [auth Q], L [auth j], M [auth n], O [auth q], R [auth T], S [auth U], U [auth W], X [auth t], Y [auth u]	IPR036253	Flavivirus glycoprotein, central and dimerisation domain superfamily	Homologous Superfamily
AA [auth w], C [auth J], D [auth N], F [auth Q], L [auth j], AA [auth w], C [auth J], D [auth N], F [auth Q], L [auth j], M [auth n], O [auth q], R [auth T], S [auth U], U [auth W], X [auth t], Y [auth u]	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
AA [auth w], C [auth J], D [auth N], F [auth Q], L [auth j], AA [auth w], C [auth J], D [auth N], F [auth Q], L [auth j], M [auth n], O [auth q], R [auth T], S [auth U], U [auth W], X [auth t], Y [auth u]	IPR042305	Alphavirus E2 glycoprotein, domain B	Homologous Superfamily
AA [auth w], C [auth J], D [auth N], F [auth Q], L [auth j], AA [auth w], C [auth J], D [auth N], F [auth Q], L [auth j], M [auth n], O [auth q], R [auth T], S [auth U], U [auth W], X [auth t], Y [auth u]	IPR042306	Alphavirus E2 glycoprotein, domain C	Homologous Superfamily
AA [auth w], C [auth J], D [auth N], F [auth Q], L [auth j], AA [auth w], C [auth J], D [auth N], F [auth Q], L [auth j], M [auth n], O [auth q], R [auth T], S [auth U], U [auth W], X [auth t], Y [auth u]	IPR000936	Alphavirus E2 glycoprotein	Family
AA [auth w], C [auth J], D [auth N], F [auth Q], L [auth j], AA [auth w], C [auth J], D [auth N], F [auth Q], L [auth j], M [auth n], O [auth q], R [auth T], S [auth U], U [auth W], X [auth t], Y [auth u]	IPR000930	Peptidase S3, togavirin	Domain
AA [auth w], C [auth J], D [auth N], F [auth Q], L [auth j], AA [auth w], C [auth J], D [auth N], F [auth Q], L [auth j], M [auth n], O [auth q], R [auth T], S [auth U], U [auth W], X [auth t], Y [auth u]	IPR002548	Alphavirus E1 glycoprotein	Domain
AA [auth w], C [auth J], D [auth N], F [auth Q], L [auth j], AA [auth w], C [auth J], D [auth N], F [auth Q], L [auth j], M [auth n], O [auth q], R [auth T], S [auth U], U [auth W], X [auth t], Y [auth u]	IPR000336	Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily	Homologous Superfamily

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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.