5N09 | pdb_00005n09

Crystal structure of L107C/A313C covalently linked dengue 2 virus envelope glycoprotein dimer in complex with the Fab fragment of the broadly neutralizing human antibody EDE2 A11

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
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)
B	Acetyltransf_1	e5n09B1	A: a/b three-layered sandwiches	X: Beta domain of coronavirus spike glycoprotein	H: HAMP domain	T: Polymerase basic protein 2 cap-binding domain	F: Acetyltransf_1	ECOD (v294.1)
A	Acetyltransf_1	e5n09A1	A: a/b three-layered sandwiches	X: Beta domain of coronavirus spike glycoprotein	H: HAMP domain	T: Polymerase basic protein 2 cap-binding domain	F: Acetyltransf_1	ECOD (v294.1)
D [auth I]	Acetyltransf_1	e5n09I1	A: a/b three-layered sandwiches	X: Beta domain of coronavirus spike glycoprotein	H: HAMP domain	T: Polymerase basic protein 2 cap-binding domain	F: Acetyltransf_1	ECOD (v294.1)
C [auth H]	Acetyltransf_1	e5n09H1	A: a/b three-layered sandwiches	X: Beta domain of coronavirus spike glycoprotein	H: HAMP domain	T: Polymerase basic protein 2 cap-binding domain	F: Acetyltransf_1	ECOD (v294.1)
F [auth M]	Acetyltransf_1	e5n09M1	A: a/b three-layered sandwiches	X: Beta domain of coronavirus spike glycoprotein	H: HAMP domain	T: Polymerase basic protein 2 cap-binding domain	F: Acetyltransf_1	ECOD (v294.1)
E [auth L]	Acetyltransf_1	e5n09L1	A: a/b three-layered sandwiches	X: Beta domain of coronavirus spike glycoprotein	H: HAMP domain	T: Polymerase basic protein 2 cap-binding domain	F: Acetyltransf_1	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.60.98.10	Mainly Beta	Sandwich	Tick-borne Encephalitis virus Glycoprotein	domain 1	CATH (4.3.0)
B	3.30.67.10	Alpha Beta	2-Layer Sandwich	Viral Envelope Glycoprotein	domain 2	CATH (4.3.0)
B	3.30.387.10	Alpha Beta	2-Layer Sandwich	Viral Envelope Glycoprotein	domain 3	CATH (4.3.0)
B	2.60.40.350	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)
A	2.60.98.10	Mainly Beta	Sandwich	Tick-borne Encephalitis virus Glycoprotein	domain 1	CATH (4.3.0)
A	3.30.67.10	Alpha Beta	2-Layer Sandwich	Viral Envelope Glycoprotein	domain 2	CATH (4.3.0)
A	3.30.387.10	Alpha Beta	2-Layer Sandwich	Viral Envelope Glycoprotein	domain 3	CATH (4.3.0)
A	2.60.40.350	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)
D [auth I]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
F [auth M]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
E [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

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 [auth H], D [auth I]	Fab EDE2 A11, broadly neutralizing	VH-CH1	Homo sapiens (human)	IGHV3-7401, IGHV3-7402, IGHV3-7403, IGHJ301, IGHG1*03	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_LAMBDA	IMGT (202612-0)
E [auth L], F [auth M]	Fab EDE2 A11, broadly neutralizing	L-LAMBDA	Homo sapiens (human)	IGLV2-2301, TRGJ7-201, TRGJ2-201, IGLC201, IGLC202, IGLC304	V-DOMAIN V-LAMBDA, C-DOMAIN C-LAMBDA	IG	FAB-GAMMA-1_LAMBDA	IMGT (202612-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
C [auth H], D [auth I]	Heavy Chain	IGHV3	-	envelope glycoprotein e	SAbDab (2026-03-27)
E [auth L], F [auth M]	Light Chain	IGLV2	Lambda	envelope glycoprotein e	SAbDab (2026-03-27)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Envelope Glycoprotein E	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	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
C [auth H], D [auth I]	BROADLY NEUTRALIZING HUMAN ANTIBODY EDE2 A11 - Heavy chain	-	-	-
E [auth L], F [auth M]	BROADLY NEUTRALIZING HUMAN ANTIBODY EDE2 A11 - Light chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

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