8JN6 | pdb_00008jn6

Cryo-EM structure of the small tail club shape particle of dengue virus serotype 3 strain CH53489 in complex with human antibody DENV-290 Fab at 37 deg C

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)
A [auth C]		e8jn6C01	A: a/b three-layered sandwiches	X: ATP-grasp_6	H: ATP-grasp_6	T: ATP-grasp_6	F:	ECOD (v294.1)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
D [auth L]	Light Chain	IGKV2	Kappa	polyprotein (fragment)	SAbDab (2026-04-10)
C [auth H]	Heavy Chain	IGHV3	-	polyprotein (fragment)	SAbDab (2026-04-10)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D [auth L]	Human antibody DENV-290 light chain	-	-	-
C [auth H]	Human antibody DENV-290 heavy chain	-	-	-
A [auth C], B [auth E]	Polyprotein (Fragment)	protein binding binding protein dimerization activity	viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell virion attachment to host cell biological process involved in interspecies interaction between organisms adhesion of symbiont to host cell viral life cycle adhesion of symbiont to host biological process involved in interaction with host biological process involved in symbiotic interaction import into cell receptor-mediated endocytosis of virus by host cell transport establishment of localization viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell virion attachment to host cell biological process involved in interspecies interaction between organisms adhesion of symbiont to host cell viral life cycle adhesion of symbiont to host biological process involved in interaction with host biological process involved in symbiotic interaction import into cell receptor-mediated endocytosis of virus by host cell transport 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 symbiont-mediated perturbation of host defense response symbiont-mediated suppression of host immune response symbiont-mediated suppression of host innate immune response symbiont-mediated perturbation of host process symbiont-mediated perturbation of host immune response symbiont-mediated perturbation of host innate immune response modulation of process of another organism	virion component virion membrane cellular anatomical structure extracellular region host intracellular membrane-bounded organelle host cellular component host intracellular part host cell endoplasmic reticulum host cell membrane other organism part host cell cytoplasm part host intracellular organelle host cell cytoplasm host cell part virion component virion membrane cellular anatomical structure extracellular region host intracellular membrane-bounded organelle host cellular component host intracellular part host cell endoplasmic reticulum host cell membrane other organism part host cell cytoplasm part host intracellular organelle host cell cytoplasm host cell part host cell endomembrane system host intracellular region host cell endoplasmic reticulum membrane viral membrane viral envelope

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth C], B [auth E]	IPR038345	Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily	Homologous Superfamily
A [auth C], B [auth E]	IPR038688	Flavivirus polyprotein propeptide superfamily	Homologous Superfamily
A [auth C], B [auth E]	IPR026470	Flavivirus envelope glycoprotein E, Stem/Anchor domain	Domain
A [auth C], B [auth E]	IPR011998	Envelope glycoprotein E, central and dimerisation domain, flavivirus	Domain
A [auth C], B [auth E]	IPR013755	Flaviviral glycoprotein E, central domain, subdomain 1	Homologous Superfamily
A [auth C], B [auth E]	IPR038055	Flaviviral glycoprotein E, dimerisation domain	Homologous Superfamily
A [auth C], B [auth E]	IPR014756	Immunoglobulin E-set	Homologous Superfamily
A [auth C], B [auth E]	IPR027287	Glycoprotein E, immunoglobulin-like domain, flavivirus	Domain
A [auth C], B [auth E]	IPR013756	Flaviviral glycoprotein E, central domain, subdomain 2	Homologous Superfamily
A [auth C], B [auth E]	IPR000336	Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily	Homologous Superfamily
A [auth C], B [auth E]	IPR038302	Envelope glycoprotein M superfamily, flavivirus	Homologous Superfamily
A [auth C], B [auth E]	IPR002535	Flavivirus polyprotein propeptide	Domain
A [auth C], B [auth E]	IPR036253	Flavivirus glycoprotein, central and dimerisation domain superfamily	Homologous Superfamily
A [auth C], B [auth E]	IPR000069	Envelope glycoprotein M, flavivirus	Domain

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.