Annotations: 8DED

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

External Resource: Annotation

Domain Annotation: ECOD Classification
SAbDab Antibody Annotation
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)
J [auth V]	Polyketide_cyc2	e8dedV1	A: beta barrels	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Polyketide_cyc2	ECOD (v294.2)
H [auth L]	LNT_N	e8dedL1	A: beta barrels	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: LNT_N	ECOD (v294.2)
I [auth U]	Polyketide_cyc2	e8dedU1	A: beta barrels	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Polyketide_cyc2	ECOD (v294.2)
G [auth H]	LNT_N	e8dedH1	A: beta barrels	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: LNT_N	ECOD (v294.2)
F [auth K]	Polyketide_cyc2	e8dedK1	A: beta barrels	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Polyketide_cyc2	ECOD (v294.2)
D [auth G]	Polyketide_cyc2	e8dedG1	A: beta barrels	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Polyketide_cyc2	ECOD (v294.2)
B	Polyketide_cyc2	e8dedB1	A: beta barrels	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Polyketide_cyc2	ECOD (v294.2)
E [auth J]	Polyketide_cyc2	e8dedJ1	A: beta barrels	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Polyketide_cyc2	ECOD (v294.2)
C [auth F]	Polyketide_cyc2	e8dedF1	A: beta barrels	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Polyketide_cyc2	ECOD (v294.2)
A	Polyketide_cyc2	e8dedA1	A: beta barrels	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Polyketide_cyc2	ECOD (v294.2)

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 (2026-05-08)
G [auth H], I [auth U]	Heavy Chain	IGHV3	-	spike glycoprotein e2 \| spike glycoprotein e1	SAbDab (2026-05-08)

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 passive transmembrane transporter activity channel activity transporter activity 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 passive transmembrane transporter activity channel activity transporter activity transmembrane transporter activity 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 transmembrane transport localization transport monoatomic ion transmembrane transport monoatomic ion transport cellular process establishment of localization 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 intracellular membrane-bounded organelle host cellular component host intracellular part host cell endoplasmic reticulum other organism part host cell cytoplasm part host intracellular organelle cellular anatomical structure host cell cytoplasm host cell part host intracellular region host cell plasma membrane host cell membrane virion component host intracellular membrane-bounded organelle host cellular component host intracellular part host cell endoplasmic reticulum other organism part host cell cytoplasm part host intracellular organelle cellular anatomical structure host cell cytoplasm host cell part host intracellular region host cell plasma membrane host cell membrane virion component virion membrane viral capsid icosahedral viral capsid T=4 icosahedral viral capsid host cell Golgi apparatus host cell nucleus
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 passive transmembrane transporter activity channel activity transporter activity 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 passive transmembrane transporter activity channel activity transporter activity transmembrane transporter activity 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 transmembrane transport localization transport monoatomic ion transmembrane transport monoatomic ion transport cellular process establishment of localization 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 intracellular membrane-bounded organelle host cellular component host intracellular part host cell endoplasmic reticulum other organism part host cell cytoplasm part host intracellular organelle cellular anatomical structure host cell cytoplasm host cell part host intracellular region host cell plasma membrane host cell membrane virion component host intracellular membrane-bounded organelle host cellular component host intracellular part host cell endoplasmic reticulum other organism part host cell cytoplasm part host intracellular organelle cellular anatomical structure host cell cytoplasm host cell part host intracellular region host cell plasma membrane host cell membrane virion component virion membrane viral capsid icosahedral viral capsid T=4 icosahedral viral capsid host cell Golgi apparatus host cell nucleus

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]	IPR043504	Peptidase_S1_PA_chymotrypsin	Unknown
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
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]	IPR043504	Peptidase_S1_PA_chymotrypsin	Unknown
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

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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.

8DED | pdb_00008ded

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

External Resource: Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

SAbDab Antibody Annotation SAbDab Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage