8DED | pdb_00008ded

Cryo-EM Structure of Western Equine Encephalitis Virus VLP in complex with SKW19 fab

External Resource: Annotation

SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
H [auth L], J [auth V]	Light Chain	IGKV2	Kappa	spike glycoprotein e2 \| spike glycoprotein e1	SAbDab (2025-10-03)
G [auth H], I [auth U]	Heavy Chain	IGHV3	-	spike glycoprotein e2 \| spike glycoprotein e1	SAbDab (2025-10-03)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D [auth G], F [auth K]	PF00943	Alphavirus E2 glycoprotein (Alpha_E2_glycop)	Alphavirus E2 glycoprotein	-	Family
A, C [auth F], E [auth J]	PF01589	Alphavirus E1 glycoprotein (Alpha_E1_glycop)	Alphavirus E1 glycoprotein	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
H [auth L], J [auth V]	SKW19 Fab light chain	-	-	-
G [auth H], I [auth U]	SKW19 Fab heavy chain	-	-	-
B, D [auth G], F [auth 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 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 entry into host cell symbiont entry into host viral life cycle 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 entry into host cell symbiont entry into host viral life cycle 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 virion attachment to host cell adhesion of symbiont to host cell adhesion of symbiont to host proteolysis metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process	cellular anatomical structure membrane host cell plasma membrane host cellular component 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 cellular anatomical structure membrane host cell plasma membrane host cellular component 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
A, C [auth F], E [auth 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 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 entry into host cell symbiont entry into host viral life cycle 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 entry into host cell symbiont entry into host viral life cycle 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 virion attachment to host cell adhesion of symbiont to host cell adhesion of symbiont to host proteolysis metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process	cellular anatomical structure membrane host cell plasma membrane host cellular component 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 cellular anatomical structure membrane host cell plasma membrane host cellular component 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

InterPro: Protein Family Classification InterPro Database Homepage

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