6XOB | pdb_00006xob

CryoEM structure of Eastern Equine Encephalitis (EEEV) VLP with Fab EEEV-143.

External Resource: Annotation

Domain Annotation: ECOD Classification
SAbDab Antibody Annotation
Protein Family 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)
T	C1-set_4	e6xobT1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
T	V-set	e6xobT2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
R	C1-set_4	e6xobR1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
R	V-set	e6xobR2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
P	C1-set_4	e6xobP2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
P	V-set	e6xobP1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
N	C1-set_4	e6xobN1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
N	V-set	e6xobN2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
S	V-set_8	e6xobS2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
S	C1-set_1	e6xobS1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
Q	V-set_8	e6xobQ1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
Q	C1-set_1	e6xobQ2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
O	V-set_8	e6xobO1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
O	C1-set_1	e6xobO2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
M	V-set_8	e6xobM1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
M	C1-set_1	e6xobM2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
L	Peptidase_S3	e6xobL1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: Peptidase_S3	ECOD (1.6)
I	Peptidase_S3	e6xobI1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: Peptidase_S3	ECOD (1.6)
F	Peptidase_S3	e6xobF1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: Peptidase_S3	ECOD (1.6)
C	Peptidase_S3	e6xobC1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: Peptidase_S3	ECOD (1.6)
J	Alpha_E1_glycop_2nd	e6xobJ1	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)
J	Alpha_E1_glycop_1st	e6xobJ2	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)
J	F_UNCLASSIFIED	e6xobJ3	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	Alpha_E1_glycop_2nd	e6xobG2	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)
G	Alpha_E1_glycop_1st	e6xobG1	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)
G	F_UNCLASSIFIED	e6xobG3	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	Alpha_E1_glycop_2nd	e6xobD3	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)
D	Alpha_E1_glycop_1st	e6xobD2	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)
D	F_UNCLASSIFIED	e6xobD1	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)
A	Alpha_E1_glycop_2nd	e6xobA3	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)
A	Alpha_E1_glycop_1st	e6xobA2	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)
A	F_UNCLASSIFIED	e6xobA1	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)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
N, P, R, T	Light Chain	IGKV3	Kappa	togavirin	SAbDab (2025-12-19)
M, O, Q, S	Heavy Chain	IGHV3	-	togavirin	SAbDab (2025-12-19)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, E, H, K	PF00943	Alphavirus E2 glycoprotein (Alpha_E2_glycop)	Alphavirus E2 glycoprotein	-	Family
A, D, G, 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
N, P, R, T	EEEV-143 Fab light chain	-	-	-
M, O, Q, S	EEEV-143 Fab heavy chain	-	-	-
C, F, I, L	Togavirin	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
B, E, H, K	Togavirin	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, D, G, J	Togavirin	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
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
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
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