6MWX

CryoEM structure of Chimeric Eastern Equine Encephalitis Virus with Fab of EEEV-69 Antibody

External Resource: Annotation

Domain Annotation: ECOD Classification
IMGT Antibody Annotation
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)
A	Alpha_E1_glycop_2nd	e6mwxA2	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	e6mwxA1	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	Alpha_E1_glycop_2nd	e6mwxE2	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	Alpha_E1_glycop_1st	e6mwxE1	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)
I	Alpha_E1_glycop_2nd	e6mwxI2	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)
I	Alpha_E1_glycop_1st	e6mwxI1	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)
M	Alpha_E1_glycop_2nd	e6mwxM2	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)
M	Alpha_E1_glycop_1st	e6mwxM1	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)
F	Alpha_E2_glycop_2nd	e6mwxF3	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Alpha_E2_glycop_2nd	ECOD (1.6)
F	Alpha_E2_glycop_1st	e6mwxF2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Alpha_E2_glycop_1st	ECOD (1.6)
F	Alpha_E2_glycop_3rd	e6mwxF1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Alpha_E2_glycop_3rd	ECOD (1.6)
B	Alpha_E2_glycop_2nd	e6mwxB3	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Alpha_E2_glycop_2nd	ECOD (1.6)
B	Alpha_E2_glycop_1st	e6mwxB1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Alpha_E2_glycop_1st	ECOD (1.6)
B	Alpha_E2_glycop_3rd	e6mwxB2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Alpha_E2_glycop_3rd	ECOD (1.6)
J	Alpha_E2_glycop_2nd	e6mwxJ2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Alpha_E2_glycop_2nd	ECOD (1.6)
J	Alpha_E2_glycop_1st	e6mwxJ3	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Alpha_E2_glycop_1st	ECOD (1.6)
J	Alpha_E2_glycop_3rd	e6mwxJ1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Alpha_E2_glycop_3rd	ECOD (1.6)
N	Alpha_E2_glycop_2nd	e6mwxN3	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Alpha_E2_glycop_2nd	ECOD (1.6)
N	Alpha_E2_glycop_1st	e6mwxN1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Alpha_E2_glycop_1st	ECOD (1.6)
N	Alpha_E2_glycop_3rd	e6mwxN2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Alpha_E2_glycop_3rd	ECOD (1.6)
C	V-set_8	e6mwxC1	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)
C	C1-set_1	e6mwxC2	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)
G	V-set_8	e6mwxG1	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)
G	C1-set_1	e6mwxG2	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)
K	V-set_8	e6mwxK1	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)
K	C1-set_1	e6mwxK2	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	e6mwxO1	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	e6mwxO2	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	C1-set	e6mwxL2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set	ECOD (1.6)
L	V-set_3	e6mwxL1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_3	ECOD (1.6)
D	C1-set	e6mwxD2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set	ECOD (1.6)
D	V-set_3	e6mwxD1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_3	ECOD (1.6)
H	C1-set	e6mwxH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set	ECOD (1.6)
H	V-set_3	e6mwxH2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_3	ECOD (1.6)
P	C1-set	e6mwxP1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set	ECOD (1.6)
P	V-set_3	e6mwxP2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_3	ECOD (1.6)

IMGT Antibody Annotation IMGT Database Homepage

Chain	Protein Name	Description	Organism Name	Gene Allele Name(s)	Domain Name(s)	Receptor Type	Receptor Description	Provenance Source
C, G, K, O	Fab EEEV-58	VH-CH1	Mus musculus (house mouse)	IGHV9-101, IGHJ201, IGHG2C01, IGHG2C02, IGHG2C*03	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-2C_LAMBDA	IMGT (202443-0)
D, H, L, P	Fab EEEV-58	L-LAMBDA	Mus musculus (house mouse)	IGLV101, IGLJ101, IGLC1*01	V-DOMAIN V-LAMBDA, C-DOMAIN C-LAMBDA	IG	FAB-GAMMA-2C_LAMBDA	IMGT (202443-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
C, G, K, O	Heavy Chain	IGHV9	-	e2	SAbDab (2024-11-01)
D, H, L, P	Light Chain	IGLV1	Lambda	e2	SAbDab (2024-11-01)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, E, I, M	PF01589	Alphavirus E1 glycoprotein (Alpha_E1_glycop)	Alphavirus E1 glycoprotein	-	Family
B, F, J, N	PF00943	Alphavirus E2 glycoprotein (Alpha_E2_glycop)	Alphavirus E2 glycoprotein	-	Family
D, H, L, P	PF07686	Immunoglobulin V-set domain (V-set)	Immunoglobulin V-set domain	This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.	Domain
D, H, L, P	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, E, I, M	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 symbiont-mediated perturbation 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 symbiont entry into host cell symbiont entry into host 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 cellular process 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 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 virion attachment to host cell adhesion of symbiont to host cell adhesion of symbiont to host 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
B, F, J, N	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 symbiont-mediated perturbation 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 symbiont entry into host cell symbiont entry into host 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 cellular process 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 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 virion attachment to host cell adhesion of symbiont to host cell adhesion of symbiont to host 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
C, G, K, O	EEEV-69 antibody heavy chain	-	-	-
D, H, L, P	EEEV-69 antibody light chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, E, I, M	IPR002533	Alphavirus E3 spike glycoprotein	Domain
A, E, I, M	IPR038055	Flaviviral glycoprotein E, dimerisation domain	Homologous Superfamily
A, E, I, M	IPR014756	Immunoglobulin E-set	Homologous Superfamily
A, E, I, M	IPR042304	Alphavirus E2 glycoprotein, domain A	Homologous Superfamily
A, E, I, M	IPR036253	Flavivirus glycoprotein, central and dimerisation domain superfamily	Homologous Superfamily
A, E, I, M	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
A, E, I, M	IPR042305	Alphavirus E2 glycoprotein, domain B	Homologous Superfamily
A, E, I, M	IPR042306	Alphavirus E2 glycoprotein, domain C	Homologous Superfamily
A, E, I, M	IPR000936	Alphavirus E2 glycoprotein	Family
A, E, I, M	IPR000930	Peptidase S3, togavirin	Domain
A, E, I, M	IPR002548	Alphavirus E1 glycoprotein	Domain
A, E, I, M	IPR000336	Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily	Homologous Superfamily
A, E, I, M	IPR043504	Peptidase S1, PA clan, chymotrypsin-like fold	Homologous Superfamily
B, F, J, N	IPR002533	Alphavirus E3 spike glycoprotein	Domain
B, F, J, N	IPR038055	Flaviviral glycoprotein E, dimerisation domain	Homologous Superfamily
B, F, J, N	IPR014756	Immunoglobulin E-set	Homologous Superfamily
B, F, J, N	IPR042304	Alphavirus E2 glycoprotein, domain A	Homologous Superfamily
B, F, J, N	IPR036253	Flavivirus glycoprotein, central and dimerisation domain superfamily	Homologous Superfamily
B, F, J, N	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
B, F, J, N	IPR042305	Alphavirus E2 glycoprotein, domain B	Homologous Superfamily
B, F, J, N	IPR042306	Alphavirus E2 glycoprotein, domain C	Homologous Superfamily
B, F, J, N	IPR000936	Alphavirus E2 glycoprotein	Family
B, F, J, N	IPR000930	Peptidase S3, togavirin	Domain
B, F, J, N	IPR002548	Alphavirus E1 glycoprotein	Domain
B, F, J, N	IPR000336	Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily	Homologous Superfamily
B, F, J, N	IPR043504	Peptidase S1, PA clan, chymotrypsin-like fold	Homologous Superfamily
D, H, L, P	IPR003597	Immunoglobulin C1-set	Domain
D, H, L, P	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
D, H, L, P	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
D, H, L, P	IPR013106	Immunoglobulin V-set domain	Domain
D, H, L, P	IPR003599	Immunoglobulin domain subtype	Domain
D, H, L, P	IPR007110	Immunoglobulin-like domain	Domain
D, H, L, P	IPR050160	Major Histocompatibility Complex/Immunoglobulin	Family
D, H, L, P	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site

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6MWX

CryoEM structure of Chimeric Eastern Equine Encephalitis Virus with Fab of EEEV-69 Antibody

External Resource: Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

IMGT Antibody Annotation IMGT Database Homepage

SAbDab Antibody Annotation SAbDab Database Homepage

Protein Family Annotation Pfam Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage