8DER | pdb_00008der

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

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
L [auth V]	Polyketide_cyc2	e8derV1	A: alpha bundles	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Polyketide_cyc2	ECOD (develop294)
J [auth L]	Polyketide_cyc2	e8derL1	A: alpha bundles	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Polyketide_cyc2	ECOD (develop294)
B [auth Y]		e8derY1	A: alpha bundles	X: RNase A-like	H: RNase A-like	T: RNase A-like	F:	ECOD (develop294)
H [auth A]	Polyketide_cyc2	e8derA1	A: alpha bundles	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Polyketide_cyc2	ECOD (develop294)
G [auth B]	Polyketide_cyc2	e8derB1	A: alpha bundles	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Polyketide_cyc2	ECOD (develop294)
E [auth C]		e8derC1	A: alpha bundles	X: RNase A-like	H: RNase A-like	T: RNase A-like	F:	ECOD (develop294)
F	Polyketide_cyc2	e8derF1	A: alpha bundles	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Polyketide_cyc2	ECOD (develop294)
D [auth E]	Polyketide_cyc2	e8derE1	A: alpha bundles	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Polyketide_cyc2	ECOD (develop294)
C [auth G]	Polyketide_cyc2	e8derG1	A: alpha bundles	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Polyketide_cyc2	ECOD (develop294)
K [auth W]	Polyketide_cyc2	e8derW1	A: alpha bundles	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Polyketide_cyc2	ECOD (develop294)
I [auth H]	Polyketide_cyc2	e8derH1	A: alpha bundles	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Polyketide_cyc2	ECOD (develop294)
A [auth X]		e8derX1	A: alpha bundles	X: RNase A-like	H: RNase A-like	T: RNase A-like	F:	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
L [auth V]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
J [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
B [auth Y]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
H [auth A]	2.60.40.3200	Mainly Beta	Sandwich	Immunoglobulin-like	Alphavirus E2 glycoprotein, A domain	CATH (utative)
H [auth A]	2.60.40.2400	Mainly Beta	Sandwich	Immunoglobulin-like	Alphavirus E2 glycoprotein, domain C	CATH (utative)
G [auth B]	2.60.40.3200	Mainly Beta	Sandwich	Immunoglobulin-like	Alphavirus E2 glycoprotein, A domain	CATH (utative)
G [auth B]	2.60.40.2400	Mainly Beta	Sandwich	Immunoglobulin-like	Alphavirus E2 glycoprotein, domain C	CATH (utative)
E [auth C]	2.60.40.3200	Mainly Beta	Sandwich	Immunoglobulin-like	Alphavirus E2 glycoprotein, A domain	CATH (utative)
E [auth C]	2.60.40.2400	Mainly Beta	Sandwich	Immunoglobulin-like	Alphavirus E2 glycoprotein, domain C	CATH (utative)
F	2.60.40.350	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (utative)
D [auth E]	2.60.40.350	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (utative)
C [auth G]	2.60.40.350	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (utative)
K [auth W]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
I [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
A [auth X]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B [auth Y], J [auth L], L [auth V]	Light Chain	IGLV3	Lambda	spike glycoprotein e2	SAbDab (2026-03-20)
A [auth X], I [auth H], K [auth W]	Heavy Chain	IGHV3	-	spike glycoprotein e2	SAbDab (2026-03-20)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth Y], J [auth L], L [auth V]	SKV16 Fab Light Chain	-	-	-
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 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-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 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-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 import into cell receptor-mediated endocytosis of virus by host cell transport viral life cycle establishment of localization vesicle-mediated transport 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 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 cell plasma membrane host cellular component cellular anatomical structure 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 cell plasma membrane host cellular component cellular anatomical structure 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 viral membrane viral envelope
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 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-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 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-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 import into cell receptor-mediated endocytosis of virus by host cell transport viral life cycle establishment of localization vesicle-mediated transport 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 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 cell plasma membrane host cellular component cellular anatomical structure 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 cell plasma membrane host cellular component cellular anatomical structure 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 viral membrane viral envelope
A [auth X], I [auth H], K [auth W]	SKV16 Fab Heavy Chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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]	IPR043504	Peptidase_S1_PA_chymotrypsin	Unknown
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
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	IPR043504	Peptidase_S1_PA_chymotrypsin	Unknown
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