7FFQ | pdb_00007ffq

Cryo-EM structure of VEEV VLP at the 2-fold axes

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: OPM

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
K [auth S]	SCOP2B Superfamily	Trypsin-like serine proteases	8044424	3000114	SCOP2B (2022-06-29)
D [auth F]	SCOP2B Superfamily	Trypsin-like serine proteases	8044424	3000114	SCOP2B (2022-06-29)
A	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)
K [auth S]	Peptidase_S3	e7ffqS1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: Peptidase_S3	ECOD (1.6)
D [auth F]	Peptidase_S3	e7ffqF1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: Peptidase_S3	ECOD (1.6)
A	Peptidase_S3	e7ffqA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: Peptidase_S3	ECOD (1.6)
E [auth G]	Alpha_E1_glycop_2nd	e7ffqG2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Alpha_E1_glycop_2nd	ECOD (1.6)
E [auth G]	Alpha_E1_glycop_1st	e7ffqG1	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: Alpha_E1_glycop_1st	ECOD (1.6)
E [auth G]	Alpha_E1_glycop_like	e7ffqG3	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: Alpha_E1_glycop_like	ECOD (1.6)
C	Alpha_E1_glycop_2nd	e7ffqC2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Alpha_E1_glycop_2nd	ECOD (1.6)
C	Alpha_E1_glycop_1st	e7ffqC1	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: Alpha_E1_glycop_1st	ECOD (1.6)
C	Alpha_E1_glycop_like	e7ffqC3	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: Alpha_E1_glycop_like	ECOD (1.6)
B	Alpha_E1_glycop_2nd	e7ffqB2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Alpha_E1_glycop_2nd	ECOD (1.6)
B	Alpha_E1_glycop_1st	e7ffqB1	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: Alpha_E1_glycop_1st	ECOD (1.6)
B	Alpha_E1_glycop_like	e7ffqB3	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: Alpha_E1_glycop_like	ECOD (1.6)
L [auth T]	Alpha_E3_glycop	e7ffqT1	A: a+b two layers	X: Glycoprotein E3 (From Topology)	H: Glycoprotein E3 (From Topology)	T: Glycoprotein E3	F: Alpha_E3_glycop	ECOD (1.6)
H [auth P]	Alpha_E3_glycop	e7ffqP1	A: a+b two layers	X: Glycoprotein E3 (From Topology)	H: Glycoprotein E3 (From Topology)	T: Glycoprotein E3	F: Alpha_E3_glycop	ECOD (1.6)
F [auth I]	Alpha_E3_glycop	e7ffqI1	A: a+b two layers	X: Glycoprotein E3 (From Topology)	H: Glycoprotein E3 (From Topology)	T: Glycoprotein E3	F: Alpha_E3_glycop	ECOD (1.6)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, D [auth F], K [auth S]	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 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 symbiont-mediated suppression of host signal transduction pathway symbiont-mediated suppression of host toll-like receptor signaling pathway symbiont-mediated perturbation of host signal transduction pathway 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 symbiont-mediated suppression of host signal transduction pathway symbiont-mediated suppression of host toll-like receptor signaling pathway symbiont-mediated perturbation of host signal transduction 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 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
B, C, E [auth G]	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 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 symbiont-mediated suppression of host signal transduction pathway symbiont-mediated suppression of host toll-like receptor signaling pathway symbiont-mediated perturbation of host signal transduction pathway 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 symbiont-mediated suppression of host signal transduction pathway symbiont-mediated suppression of host toll-like receptor signaling pathway symbiont-mediated perturbation of host signal transduction 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 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
F [auth I], H [auth P], L [auth T]	assembly protein E3	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 symbiont-mediated suppression of host signal transduction pathway symbiont-mediated suppression of host toll-like receptor signaling pathway symbiont-mediated perturbation of host signal transduction pathway 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 symbiont-mediated suppression of host signal transduction pathway symbiont-mediated suppression of host toll-like receptor signaling pathway symbiont-mediated perturbation of host signal transduction 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 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 J], I [auth Q], J [auth R]	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 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 symbiont-mediated suppression of host signal transduction pathway symbiont-mediated suppression of host toll-like receptor signaling pathway symbiont-mediated perturbation of host signal transduction pathway 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 symbiont-mediated suppression of host signal transduction pathway symbiont-mediated suppression of host toll-like receptor signaling pathway symbiont-mediated perturbation of host signal transduction 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 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, D [auth F], K [auth S]	IPR002533	Alphavirus E3 spike glycoprotein	Domain
A, D [auth F], K [auth S]	IPR038055	Flaviviral glycoprotein E, dimerisation domain	Homologous Superfamily
A, D [auth F], K [auth S]	IPR014756	Immunoglobulin E-set	Homologous Superfamily
A, D [auth F], K [auth S]	IPR042304	Alphavirus E2 glycoprotein, domain A	Homologous Superfamily
A, D [auth F], K [auth S]	IPR036253	Flavivirus glycoprotein, central and dimerisation domain superfamily	Homologous Superfamily
A, D [auth F], K [auth S]	IPR043504	Peptidase_S1_PA_chymotrypsin	Unknown
A, D [auth F], K [auth S]	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
A, D [auth F], K [auth S]	IPR042305	Alphavirus E2 glycoprotein, domain B	Homologous Superfamily
A, D [auth F], K [auth S]	IPR042306	Alphavirus E2 glycoprotein, domain C	Homologous Superfamily
A, D [auth F], K [auth S]	IPR000936	Alphavirus E2 glycoprotein	Family
A, D [auth F], K [auth S]	IPR000930	Peptidase S3, togavirin	Domain
A, D [auth F], K [auth S]	IPR002548	Alphavirus E1 glycoprotein	Domain
A, D [auth F], K [auth S]	IPR000336	Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily	Homologous Superfamily
B, C, E [auth G]	IPR002533	Alphavirus E3 spike glycoprotein	Domain
B, C, E [auth G]	IPR038055	Flaviviral glycoprotein E, dimerisation domain	Homologous Superfamily
B, C, E [auth G]	IPR014756	Immunoglobulin E-set	Homologous Superfamily
B, C, E [auth G]	IPR042304	Alphavirus E2 glycoprotein, domain A	Homologous Superfamily
B, C, E [auth G]	IPR036253	Flavivirus glycoprotein, central and dimerisation domain superfamily	Homologous Superfamily
B, C, E [auth G]	IPR043504	Peptidase_S1_PA_chymotrypsin	Unknown
B, C, E [auth G]	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
B, C, E [auth G]	IPR042305	Alphavirus E2 glycoprotein, domain B	Homologous Superfamily
B, C, E [auth G]	IPR042306	Alphavirus E2 glycoprotein, domain C	Homologous Superfamily
B, C, E [auth G]	IPR000936	Alphavirus E2 glycoprotein	Family
B, C, E [auth G]	IPR000930	Peptidase S3, togavirin	Domain
B, C, E [auth G]	IPR002548	Alphavirus E1 glycoprotein	Domain
B, C, E [auth G]	IPR000336	Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily	Homologous Superfamily
F [auth I], H [auth P], L [auth T]	IPR002533	Alphavirus E3 spike glycoprotein	Domain
F [auth I], H [auth P], L [auth T]	IPR038055	Flaviviral glycoprotein E, dimerisation domain	Homologous Superfamily
F [auth I], H [auth P], L [auth T]	IPR014756	Immunoglobulin E-set	Homologous Superfamily
F [auth I], H [auth P], L [auth T]	IPR042304	Alphavirus E2 glycoprotein, domain A	Homologous Superfamily
F [auth I], H [auth P], L [auth T]	IPR036253	Flavivirus glycoprotein, central and dimerisation domain superfamily	Homologous Superfamily
F [auth I], H [auth P], L [auth T]	IPR043504	Peptidase_S1_PA_chymotrypsin	Unknown
F [auth I], H [auth P], L [auth T]	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
F [auth I], H [auth P], L [auth T]	IPR042305	Alphavirus E2 glycoprotein, domain B	Homologous Superfamily
F [auth I], H [auth P], L [auth T]	IPR042306	Alphavirus E2 glycoprotein, domain C	Homologous Superfamily
F [auth I], H [auth P], L [auth T]	IPR000936	Alphavirus E2 glycoprotein	Family
F [auth I], H [auth P], L [auth T]	IPR000930	Peptidase S3, togavirin	Domain
F [auth I], H [auth P], L [auth T]	IPR002548	Alphavirus E1 glycoprotein	Domain
F [auth I], H [auth P], L [auth T]	IPR000336	Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily	Homologous Superfamily
G [auth J], I [auth Q], J [auth R]	IPR002533	Alphavirus E3 spike glycoprotein	Domain
G [auth J], I [auth Q], J [auth R]	IPR038055	Flaviviral glycoprotein E, dimerisation domain	Homologous Superfamily
G [auth J], I [auth Q], J [auth R]	IPR014756	Immunoglobulin E-set	Homologous Superfamily
G [auth J], I [auth Q], J [auth R]	IPR042304	Alphavirus E2 glycoprotein, domain A	Homologous Superfamily
G [auth J], I [auth Q], J [auth R]	IPR036253	Flavivirus glycoprotein, central and dimerisation domain superfamily	Homologous Superfamily
G [auth J], I [auth Q], J [auth R]	IPR043504	Peptidase_S1_PA_chymotrypsin	Unknown
G [auth J], I [auth Q], J [auth R]	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
G [auth J], I [auth Q], J [auth R]	IPR042305	Alphavirus E2 glycoprotein, domain B	Homologous Superfamily
G [auth J], I [auth Q], J [auth R]	IPR042306	Alphavirus E2 glycoprotein, domain C	Homologous Superfamily
G [auth J], I [auth Q], J [auth R]	IPR000936	Alphavirus E2 glycoprotein	Family
G [auth J], I [auth Q], J [auth R]	IPR000930	Peptidase S3, togavirin	Domain
G [auth J], I [auth Q], J [auth R]	IPR002548	Alphavirus E1 glycoprotein	Domain
G [auth J], I [auth Q], J [auth R]	IPR000336	Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily	Homologous Superfamily

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B, C, D [auth F], E [auth G] A, B, C, D [auth F], E [auth G], F [auth I], G [auth J], H [auth P], I [auth Q], J [auth R], K [auth S], L [auth T]	OPM	Transmembrane	Bitopic proteins	Viral membrane fusion glycoprotein	Alphavirus E1 glycoprotein