8DER

Cryo-EM local refinement of antibody SKV16 in complex with VEEV alphavirus spike glycoprotein

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)
A [auth X]	PF07686	e8derX1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
I [auth H]	PF07686	e8derH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
K [auth W]	PF07686	e8derW1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
B [auth Y]	PF07686	e8derY1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
J [auth L]	PF07686	e8derL1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
L [auth V]	PF07686	e8derV1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
C [auth G]	PF01589	e8derG2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF01589	ECOD (1.6)
C [auth G]	PF01589	e8derG1	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: PF01589	ECOD (1.6)
D [auth E]	PF01589	e8derE1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF01589	ECOD (1.6)
D [auth E]	PF01589	e8derE2	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: PF01589	ECOD (1.6)
F	PF01589	e8derF2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF01589	ECOD (1.6)
F	PF01589	e8derF1	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: PF01589	ECOD (1.6)
E [auth C]	PF00943	e8derC1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF00943	ECOD (1.6)
G [auth B]	PF00943	e8derB1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF00943	ECOD (1.6)
H [auth A]	PF00943	e8derA2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF00943	ECOD (1.6)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A [auth X], I [auth H], K [auth W]	Heavy Chain	IGHV3	-	spike glycoprotein e2	SAbDab (2024-05-03)
B [auth Y], J [auth L], L [auth V]	Light Chain	IGLV3	Lambda	spike glycoprotein e2	SAbDab (2024-05-03)

Protein Family Annotation Pfam Database Homepage

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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth X], I [auth H], K [auth W]	SKV16 Fab Heavy Chain	-	-	-
B [auth Y], J [auth L], L [auth V]	SKV16 Fab Light Chain	-	-	-
C [auth G], D [auth E], F	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 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 import into cell receptor-mediated endocytosis of virus by host cell biological process involved in interspecies interaction between organisms transport viral life cycle establishment of localization vesicle-mediated transport biological process involved in interaction with host biological process involved in symbiotic interaction localization symbiont entry into host cell viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell import into cell receptor-mediated endocytosis of virus by host cell biological process involved in interspecies interaction between organisms transport viral life cycle establishment of localization vesicle-mediated transport biological process involved in interaction with host biological process involved in symbiotic interaction 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 transport of virus symbiont-mediated perturbation of host cellular process symbiont-mediated suppression of host gene expression modulation by symbiont of host process symbiont-mediated perturbation of host gene expression modulation of process of another organism virion attachment to host cell adhesion of symbiont to host cell adhesion of symbiont to host 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 organic substance metabolic process organonitrogen compound metabolic process 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 viral membrane viral envelope
E [auth C], G [auth B], H [auth A]	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 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 import into cell receptor-mediated endocytosis of virus by host cell biological process involved in interspecies interaction between organisms transport viral life cycle establishment of localization vesicle-mediated transport biological process involved in interaction with host biological process involved in symbiotic interaction localization symbiont entry into host cell viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell import into cell receptor-mediated endocytosis of virus by host cell biological process involved in interspecies interaction between organisms transport viral life cycle establishment of localization vesicle-mediated transport biological process involved in interaction with host biological process involved in symbiotic interaction 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 transport of virus symbiont-mediated perturbation of host cellular process symbiont-mediated suppression of host gene expression modulation by symbiont of host process symbiont-mediated perturbation of host gene expression modulation of process of another organism virion attachment to host cell adhesion of symbiont to host cell adhesion of symbiont to host 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 organic substance metabolic process organonitrogen compound metabolic process 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 viral membrane viral envelope

InterPro: Protein Family Classification InterPro Database Homepage

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