7SFW

CryoEM structure of Venezuelan Equine Encephalitis virus (VEEV) TC-83 strain VLP in complex with Fab hVEEV-63 (focus refine of the asymmetric unit)

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: OPM
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: MemProtMD

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	Trypsin-like serine proteases	8044424	3000114	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Trypsin-like serine proteases	8044424	3000114	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Trypsin-like serine proteases	8044424	3000114	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Trypsin-like serine proteases	8044424	3000114	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	PF01589	e7sfwA3	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF01589	ECOD (1.6)
A	PF01589	e7sfwA2	A: beta complex topology	X: Viral glycoprotein, central and dimerisation domains-like	H: Viral glycoprotein, central and dimerisation domains (From Topology)	T: Viral glycoprotein, central and dimerisation domains	F: PF01589	ECOD (1.6)
A	F_UNCLASSIFIED	e7sfwA1	A: extended segments	X: Transmembrane helix of E1 envelope glycoprotein (From Topology)	H: Transmembrane helix of E1 envelope glycoprotein (From Topology)	T: Transmembrane helix of E1 envelope glycoprotein	F: F_UNCLASSIFIED	ECOD (1.6)
D	PF01589	e7sfwD3	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF01589	ECOD (1.6)
D	PF01589	e7sfwD2	A: beta complex topology	X: Viral glycoprotein, central and dimerisation domains-like	H: Viral glycoprotein, central and dimerisation domains (From Topology)	T: Viral glycoprotein, central and dimerisation domains	F: PF01589	ECOD (1.6)
D	F_UNCLASSIFIED	e7sfwD1	A: extended segments	X: Transmembrane helix of E1 envelope glycoprotein (From Topology)	H: Transmembrane helix of E1 envelope glycoprotein (From Topology)	T: Transmembrane helix of E1 envelope glycoprotein	F: F_UNCLASSIFIED	ECOD (1.6)
G	PF01589	e7sfwG3	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF01589	ECOD (1.6)
G	PF01589	e7sfwG2	A: beta complex topology	X: Viral glycoprotein, central and dimerisation domains-like	H: Viral glycoprotein, central and dimerisation domains (From Topology)	T: Viral glycoprotein, central and dimerisation domains	F: PF01589	ECOD (1.6)
G	F_UNCLASSIFIED	e7sfwG1	A: extended segments	X: Transmembrane helix of E1 envelope glycoprotein (From Topology)	H: Transmembrane helix of E1 envelope glycoprotein (From Topology)	T: Transmembrane helix of E1 envelope glycoprotein	F: F_UNCLASSIFIED	ECOD (1.6)
J	PF01589	e7sfwJ2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF01589	ECOD (1.6)
J	PF01589	e7sfwJ1	A: beta complex topology	X: Viral glycoprotein, central and dimerisation domains-like	H: Viral glycoprotein, central and dimerisation domains (From Topology)	T: Viral glycoprotein, central and dimerisation domains	F: PF01589	ECOD (1.6)
J	F_UNCLASSIFIED	e7sfwJ3	A: extended segments	X: Transmembrane helix of E1 envelope glycoprotein (From Topology)	H: Transmembrane helix of E1 envelope glycoprotein (From Topology)	T: Transmembrane helix of E1 envelope glycoprotein	F: F_UNCLASSIFIED	ECOD (1.6)
C	PF00944	e7sfwC1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: PF00944	ECOD (1.6)
F	PF00944	e7sfwF1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: PF00944	ECOD (1.6)
I	PF00944	e7sfwI1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: PF00944	ECOD (1.6)
L	PF00944	e7sfwL1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: PF00944	ECOD (1.6)
M	PF07686	e7sfwM1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
O	PF07686	e7sfwO1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
Q	PF07686	e7sfwQ1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
S	PF07686	e7sfwS1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
N	PF07686	e7sfwN1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
P	PF07686	e7sfwP1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
R	PF07686	e7sfwR1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
T	PF07686	e7sfwT1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
M, O, Q, S	Heavy Chain	IGHV1	-	spike glycoprotein e2	SAbDab (2024-06-07)
N, P, R, T	Light Chain	IGLV3	Lambda	spike glycoprotein e2	SAbDab (2024-06-07)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, D, G, J	PF01589	Alphavirus E1 glycoprotein (Alpha_E1_glycop)	Alphavirus E1 glycoprotein	-	Family
B, E, H, K	PF00943	Alphavirus E2 glycoprotein (Alpha_E2_glycop)	Alphavirus E2 glycoprotein	-	Family
C, F, I, L	PF00944	Alphavirus core protein (Peptidase_S3)	Alphavirus core protein	Also known as coat protein C and capsid protein C. This makes the literature very confusing. Alphaviruses consist of a nucleoprotein core, a lipid membrane which envelopes the core, and glycoprotein spikes protruding from the lipid membrane.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, D, G, J	Spike glycoprotein E1	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 organic cyclic compound 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 modulation by symbiont of host process symbiont-mediated perturbation of host gene expression cellular process modulation of process of another organism biological process involved in interaction with host biological process involved in symbiotic interaction response to stimulus response to biotic stimulus 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 modulation by symbiont of host process symbiont-mediated perturbation of host gene expression cellular process modulation of process of another organism biological process involved in interaction with host biological process involved in symbiotic interaction response to stimulus response to biotic stimulus symbiont-mediated suppression of host immune response symbiont-mediated suppression of host innate immune response response to host immune response symbiont-mediated suppression of host defenses symbiont-mediated perturbation of host innate immune response response to host response to external biotic stimulus symbiont-mediated perturbation of host signal transduction pathway symbiont-mediated perturbation of host defense response response to host defenses response to other organism symbiont-mediated perturbation of host immune response response to defenses of other organism symbiont-mediated perturbation of host defenses response to external stimulus symbiont-mediated suppression of host signal transduction pathway symbiont-mediated suppression of host toll-like receptor signaling pathway 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 clathrin-dependent endocytosis of virus by host cell receptor-mediated endocytosis endocytosis endocytosis involved in viral entry into host cell transport of virus virion attachment to host cell adhesion of symbiont to host cell adhesion of symbiont to host organic substance metabolic process organonitrogen compound metabolic process proteolysis metabolic process primary metabolic process protein metabolic process macromolecule metabolic process	membrane cellular anatomical entity host cell plasma membrane host cellular component host cell part host cell membrane host intracellular part host cell cytoplasm host intracellular region virion component virion membrane viral capsid icosahedral viral capsid T=4 icosahedral viral capsid membrane cellular anatomical entity host cell plasma membrane host cellular component host cell part host cell membrane 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
B, E, H, K	Spike glycoprotein E2	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 organic cyclic compound 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 modulation by symbiont of host process symbiont-mediated perturbation of host gene expression cellular process modulation of process of another organism biological process involved in interaction with host biological process involved in symbiotic interaction response to stimulus response to biotic stimulus 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 modulation by symbiont of host process symbiont-mediated perturbation of host gene expression cellular process modulation of process of another organism biological process involved in interaction with host biological process involved in symbiotic interaction response to stimulus response to biotic stimulus symbiont-mediated suppression of host immune response symbiont-mediated suppression of host innate immune response response to host immune response symbiont-mediated suppression of host defenses symbiont-mediated perturbation of host innate immune response response to host response to external biotic stimulus symbiont-mediated perturbation of host signal transduction pathway symbiont-mediated perturbation of host defense response response to host defenses response to other organism symbiont-mediated perturbation of host immune response response to defenses of other organism symbiont-mediated perturbation of host defenses response to external stimulus symbiont-mediated suppression of host signal transduction pathway symbiont-mediated suppression of host toll-like receptor signaling pathway 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 clathrin-dependent endocytosis of virus by host cell receptor-mediated endocytosis endocytosis endocytosis involved in viral entry into host cell transport of virus virion attachment to host cell adhesion of symbiont to host cell adhesion of symbiont to host organic substance metabolic process organonitrogen compound metabolic process proteolysis metabolic process primary metabolic process protein metabolic process macromolecule metabolic process	membrane cellular anatomical entity host cell plasma membrane host cellular component host cell part host cell membrane host intracellular part host cell cytoplasm host intracellular region virion component virion membrane viral capsid icosahedral viral capsid T=4 icosahedral viral capsid membrane cellular anatomical entity host cell plasma membrane host cellular component host cell part host cell membrane 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
C, F, I, L	Capsid protein	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 organic cyclic compound 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 modulation by symbiont of host process symbiont-mediated perturbation of host gene expression cellular process modulation of process of another organism biological process involved in interaction with host biological process involved in symbiotic interaction response to stimulus response to biotic stimulus 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 modulation by symbiont of host process symbiont-mediated perturbation of host gene expression cellular process modulation of process of another organism biological process involved in interaction with host biological process involved in symbiotic interaction response to stimulus response to biotic stimulus symbiont-mediated suppression of host immune response symbiont-mediated suppression of host innate immune response response to host immune response symbiont-mediated suppression of host defenses symbiont-mediated perturbation of host innate immune response response to host response to external biotic stimulus symbiont-mediated perturbation of host signal transduction pathway symbiont-mediated perturbation of host defense response response to host defenses response to other organism symbiont-mediated perturbation of host immune response response to defenses of other organism symbiont-mediated perturbation of host defenses response to external stimulus symbiont-mediated suppression of host signal transduction pathway symbiont-mediated suppression of host toll-like receptor signaling pathway 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 clathrin-dependent endocytosis of virus by host cell receptor-mediated endocytosis endocytosis endocytosis involved in viral entry into host cell transport of virus virion attachment to host cell adhesion of symbiont to host cell adhesion of symbiont to host organic substance metabolic process organonitrogen compound metabolic process proteolysis metabolic process primary metabolic process protein metabolic process macromolecule metabolic process	membrane cellular anatomical entity host cell plasma membrane host cellular component host cell part host cell membrane host intracellular part host cell cytoplasm host intracellular region virion component virion membrane viral capsid icosahedral viral capsid T=4 icosahedral viral capsid membrane cellular anatomical entity host cell plasma membrane host cellular component host cell part host cell membrane 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
M, O, Q, S	hVEEV-63 Fab heavy chain	-	-	-
N, P, R, T	hVEEV-63 Fab light chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, D, G, J	IPR002533	Alphavirus E3 spike glycoprotein	Domain
A, D, G, J	IPR038055	Flaviviral glycoprotein E, dimerisation domain	Homologous Superfamily
A, D, G, J	IPR014756	Immunoglobulin E-set	Homologous Superfamily
A, D, G, J	IPR042304	Alphavirus E2 glycoprotein, domain A	Homologous Superfamily
A, D, G, J	IPR036253	Flavivirus glycoprotein, central and dimerisation domain superfamily	Homologous Superfamily
A, D, G, J	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
A, D, G, J	IPR042305	Alphavirus E2 glycoprotein, domain B	Homologous Superfamily
A, D, G, J	IPR042306	Alphavirus E2 glycoprotein, domain C	Homologous Superfamily
A, D, G, J	IPR000936	Alphavirus E2 glycoprotein	Family
A, D, G, J	IPR000930	Peptidase S3, togavirin	Domain
A, D, G, J	IPR002548	Alphavirus E1 glycoprotein	Domain
A, D, G, J	IPR000336	Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily	Homologous Superfamily
A, D, G, J	IPR043504	Peptidase S1, PA clan, chymotrypsin-like fold	Homologous Superfamily
B, E, H, K	IPR002533	Alphavirus E3 spike glycoprotein	Domain
B, E, H, K	IPR038055	Flaviviral glycoprotein E, dimerisation domain	Homologous Superfamily
B, E, H, K	IPR014756	Immunoglobulin E-set	Homologous Superfamily
B, E, H, K	IPR042304	Alphavirus E2 glycoprotein, domain A	Homologous Superfamily
B, E, H, K	IPR036253	Flavivirus glycoprotein, central and dimerisation domain superfamily	Homologous Superfamily
B, E, H, K	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
B, E, H, K	IPR042305	Alphavirus E2 glycoprotein, domain B	Homologous Superfamily
B, E, H, K	IPR042306	Alphavirus E2 glycoprotein, domain C	Homologous Superfamily
B, E, H, K	IPR000936	Alphavirus E2 glycoprotein	Family
B, E, H, K	IPR000930	Peptidase S3, togavirin	Domain
B, E, H, K	IPR002548	Alphavirus E1 glycoprotein	Domain
B, E, H, K	IPR000336	Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily	Homologous Superfamily
B, E, H, K	IPR043504	Peptidase S1, PA clan, chymotrypsin-like fold	Homologous Superfamily
C, F, I, L	IPR002533	Alphavirus E3 spike glycoprotein	Domain
C, F, I, L	IPR038055	Flaviviral glycoprotein E, dimerisation domain	Homologous Superfamily
C, F, I, L	IPR014756	Immunoglobulin E-set	Homologous Superfamily
C, F, I, L	IPR042304	Alphavirus E2 glycoprotein, domain A	Homologous Superfamily
C, F, I, L	IPR036253	Flavivirus glycoprotein, central and dimerisation domain superfamily	Homologous Superfamily
C, F, I, L	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
C, F, I, L	IPR042305	Alphavirus E2 glycoprotein, domain B	Homologous Superfamily
C, F, I, L	IPR042306	Alphavirus E2 glycoprotein, domain C	Homologous Superfamily
C, F, I, L	IPR000936	Alphavirus E2 glycoprotein	Family
C, F, I, L	IPR000930	Peptidase S3, togavirin	Domain
C, F, I, L	IPR002548	Alphavirus E1 glycoprotein	Domain
C, F, I, L	IPR000336	Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily	Homologous Superfamily
C, F, I, L	IPR043504	Peptidase S1, PA clan, chymotrypsin-like fold	Homologous Superfamily