3J6U | pdb_00003j6u

Cryo-EM structure of Dengue virus serotype 3 in complex with human antibody 5J7 Fab

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)
H [auth L]	V-set	e3j6uL1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
G [auth H]	V-set_12	e3j6uH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)
F	Flavi_M	e3j6uF1	A: extended segments	X: Small envelope protein M (From Topology)	H: Small envelope protein M (From Topology)	T: Small envelope protein M	F: Flavi_M	ECOD (1.6)
D	Flavi_M	e3j6uD1	A: extended segments	X: Small envelope protein M (From Topology)	H: Small envelope protein M (From Topology)	T: Small envelope protein M	F: Flavi_M	ECOD (1.6)
B	Flavi_M	e3j6uB1	A: extended segments	X: Small envelope protein M (From Topology)	H: Small envelope protein M (From Topology)	T: Small envelope protein M	F: Flavi_M	ECOD (1.6)
E	Flavi_glycop_C	e3j6uE2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Flavi_glycop_C	ECOD (1.6)
E	Flavi_glycoprot	e3j6uE1	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: Flavi_glycoprot	ECOD (1.6)
E	flavi_E_stem	e3j6uE3	A: alpha arrays	X: Transmembrane domain of envelope protein E (From Topology)	H: Transmembrane domain of envelope protein E (From Topology)	T: Transmembrane domain of envelope protein E	F: flavi_E_stem	ECOD (1.6)
C	Flavi_glycop_C	e3j6uC2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Flavi_glycop_C	ECOD (1.6)
C	Flavi_glycoprot	e3j6uC1	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: Flavi_glycoprot	ECOD (1.6)
C	flavi_E_stem	e3j6uC3	A: alpha arrays	X: Transmembrane domain of envelope protein E (From Topology)	H: Transmembrane domain of envelope protein E (From Topology)	T: Transmembrane domain of envelope protein E	F: flavi_E_stem	ECOD (1.6)
A	Flavi_glycop_C	e3j6uA2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Flavi_glycop_C	ECOD (1.6)
A	Flavi_glycoprot	e3j6uA1	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: Flavi_glycoprot	ECOD (1.6)
A	flavi_E_stem	e3j6uA3	A: alpha arrays	X: Transmembrane domain of envelope protein E (From Topology)	H: Transmembrane domain of envelope protein E (From Topology)	T: Transmembrane domain of envelope protein E	F: flavi_E_stem	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
H [auth L]	Fab 5J7	V-KAPPA	Homo sapiens (human)	IGKV1-3901, IGKV1D-3901, IGKJ101, IGKJ201, IGKJ3*01	V-DOMAIN V-KAPPA	IG	FV-HEAVY_KAPPA	IMGT (202549-0)
G [auth H]	Fab 5J7	VH	Homo sapiens (human)	IGHV1-6906, IGHV1-6914, IGHJ3*02	V-DOMAIN VH	IG	FV-HEAVY_KAPPA	IMGT (202549-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
H [auth L]	Light Chain	IGKV1	Kappa	envelope protein \| envelope protein	SAbDab (2025-12-19)
G [auth H]	Heavy Chain	IGHV1	-	envelope protein \| envelope protein	SAbDab (2025-12-19)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D, F	PF01004	Flavivirus envelope glycoprotein M (Flavi_M)	Flavivirus envelope glycoprotein M	-	Family
A, C, E	PF00869	Flavivirus glycoprotein, central and dimerisation domains (Flavi_glycoprot)	Flavivirus glycoprotein, central and dimerisation domains		Domain
A, C, E	PF21659	Flavivirus envelope glycoprotein E, stem/anchor domain (Flavi_E_stem)	Flavivirus envelope glycoprotein E, stem/anchor domain	This entry represents the stem/anchor domain found at the C-terminal of envelope glycoprotein E from Flavivirus. This domain comprises a stem region followed by two transmembrane anchor domains [1-5].	Domain
A, C, E	PF02832	Flavivirus glycoprotein, immunoglobulin-like domain (Flavi_glycop_C)	Flavivirus glycoprotein, immunoglobulin-like domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
H [auth L]	Fab 5J7 light chain	-	-	-
G [auth H]	Fab 5J7 heavy chain	-	-	-
B, D, F	membrane protein	RNA methyltransferase activity O-methyltransferase activity methyltransferase cap1 activity catalytic activity, acting on RNA transferase activity, transferring one-carbon groups catalytic activity, acting on a nucleic acid transferase activity methyltransferase activity catalytic activity RNA binding double-stranded RNA binding binding nucleic acid binding RNA-directed RNA polymerase activity RNA methyltransferase activity O-methyltransferase activity methyltransferase cap1 activity catalytic activity, acting on RNA transferase activity, transferring one-carbon groups catalytic activity, acting on a nucleic acid transferase activity methyltransferase activity catalytic activity RNA binding double-stranded RNA binding binding nucleic acid binding RNA-directed RNA polymerase activity 5'-3' RNA polymerase activity RNA polymerase activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups peptidase activity catalytic activity, acting on a protein serine hydrolase activity serine-type peptidase activity hydrolase activity serine-type endopeptidase activity endopeptidase activity adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding pyrophosphatase activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity, acting on acid anhydrides nucleic acid conformation isomerase activity isomerase activity helicase activity RNA helicase activity ATP-dependent activity, acting on RNA macromolecular conformation isomerase activity ATP-dependent activity protein binding protein dimerization activity cation binding metal ion binding S-adenosylmethionine-dependent methyltransferase activity mRNA 5'-cap (guanine-N7-)-methyltransferase activity N-methyltransferase activity mRNA methyltransferase activity lipid binding passive transmembrane transporter activity channel activity transporter activity transmembrane transporter activity structural molecule activity	RNA metabolic process viral life cycle primary metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process viral genome replication biosynthetic process viral RNA genome replication viral process metabolic process RNA metabolic process viral life cycle primary metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process viral genome replication biosynthetic process viral RNA genome replication viral process metabolic process cellular process macromolecule metabolic process symbiont-mediated perturbation of host cellular process biological process involved in interspecies interaction between organisms symbiont-mediated perturbation of host process symbiont-mediated perturbation of host autophagy modulation of process of another organism symbiont-mediated activation of host autophagy 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 interferon-mediated signaling pathway symbiont-mediated suppression of host type I interferon-mediated signaling pathway symbiont-mediated perturbation of host signal transduction pathway fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell symbiont-mediated suppression of host JAK-STAT cascade symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT activity 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 clathrin-dependent endocytosis of virus by host cell receptor-mediated endocytosis endocytosis endocytosis involved in viral entry into host cell transmembrane transport monoatomic ion transmembrane transport monoatomic ion transport symbiont-mediated perturbation of host defense response symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity symbiont-mediated suppression of host pathogen-associated molecular pattern receptor signaling pathway symbiont-mediated perturbation of host immune response symbiont-mediated suppression of host immune response symbiont-mediated suppression of host innate immune response symbiont-mediated perturbation of host innate immune response symbiont-mediated suppression of cytoplasmic pattern recognition receptor signaling pathway virion attachment to host cell adhesion of symbiont to host cell adhesion of symbiont to host symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity proteolysis protein metabolic process	cellular anatomical structure membrane host intracellular membrane-bounded organelle host cellular component host intracellular part other organism part host cell mitochondrion host cell cytoplasm part host intracellular organelle host cell cytoplasm host cell part host intracellular region host cell endoplasmic reticulum host cell membrane cellular anatomical structure membrane host intracellular membrane-bounded organelle host cellular component host intracellular part other organism part host cell mitochondrion host cell cytoplasm part host intracellular organelle host cell cytoplasm host cell part host intracellular region host cell endoplasmic reticulum host cell membrane host cell endomembrane system host cell endoplasmic reticulum membrane viral capsid virion component virion membrane extracellular region host cell nucleus viral membrane viral envelope
A, C, E	envelope protein	RNA methyltransferase activity O-methyltransferase activity methyltransferase cap1 activity catalytic activity, acting on RNA transferase activity, transferring one-carbon groups catalytic activity, acting on a nucleic acid transferase activity methyltransferase activity catalytic activity RNA binding double-stranded RNA binding binding nucleic acid binding RNA-directed RNA polymerase activity RNA methyltransferase activity O-methyltransferase activity methyltransferase cap1 activity catalytic activity, acting on RNA transferase activity, transferring one-carbon groups catalytic activity, acting on a nucleic acid transferase activity methyltransferase activity catalytic activity RNA binding double-stranded RNA binding binding nucleic acid binding RNA-directed RNA polymerase activity 5'-3' RNA polymerase activity RNA polymerase activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups peptidase activity catalytic activity, acting on a protein serine hydrolase activity serine-type peptidase activity hydrolase activity serine-type endopeptidase activity endopeptidase activity adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding pyrophosphatase activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity, acting on acid anhydrides nucleic acid conformation isomerase activity isomerase activity helicase activity RNA helicase activity ATP-dependent activity, acting on RNA macromolecular conformation isomerase activity ATP-dependent activity protein binding protein dimerization activity cation binding metal ion binding S-adenosylmethionine-dependent methyltransferase activity mRNA 5'-cap (guanine-N7-)-methyltransferase activity N-methyltransferase activity mRNA methyltransferase activity lipid binding passive transmembrane transporter activity channel activity transporter activity transmembrane transporter activity structural molecule activity	RNA metabolic process viral life cycle primary metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process viral genome replication biosynthetic process viral RNA genome replication viral process metabolic process RNA metabolic process viral life cycle primary metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process viral genome replication biosynthetic process viral RNA genome replication viral process metabolic process cellular process macromolecule metabolic process symbiont-mediated perturbation of host cellular process biological process involved in interspecies interaction between organisms symbiont-mediated perturbation of host process symbiont-mediated perturbation of host autophagy modulation of process of another organism symbiont-mediated activation of host autophagy 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 interferon-mediated signaling pathway symbiont-mediated suppression of host type I interferon-mediated signaling pathway symbiont-mediated perturbation of host signal transduction pathway fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell symbiont-mediated suppression of host JAK-STAT cascade symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT activity 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 clathrin-dependent endocytosis of virus by host cell receptor-mediated endocytosis endocytosis endocytosis involved in viral entry into host cell transmembrane transport monoatomic ion transmembrane transport monoatomic ion transport symbiont-mediated perturbation of host defense response symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity symbiont-mediated suppression of host pathogen-associated molecular pattern receptor signaling pathway symbiont-mediated perturbation of host immune response symbiont-mediated suppression of host immune response symbiont-mediated suppression of host innate immune response symbiont-mediated perturbation of host innate immune response symbiont-mediated suppression of cytoplasmic pattern recognition receptor signaling pathway virion attachment to host cell adhesion of symbiont to host cell adhesion of symbiont to host symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity proteolysis protein metabolic process	cellular anatomical structure membrane host intracellular membrane-bounded organelle host cellular component host intracellular part other organism part host cell mitochondrion host cell cytoplasm part host intracellular organelle host cell cytoplasm host cell part host intracellular region host cell endoplasmic reticulum host cell membrane cellular anatomical structure membrane host intracellular membrane-bounded organelle host cellular component host intracellular part other organism part host cell mitochondrion host cell cytoplasm part host intracellular organelle host cell cytoplasm host cell part host intracellular region host cell endoplasmic reticulum host cell membrane host cell endomembrane system host cell endoplasmic reticulum membrane viral capsid virion component virion membrane extracellular region host cell nucleus viral membrane viral envelope

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D, F	IPR000208	RNA-directed RNA polymerase, fingers/palm subdomains, flavivirus	Domain
B, D, F	IPR014756	Immunoglobulin E-set	Homologous Superfamily
B, D, F	IPR001122	Capsid protein C, flavivirus	Domain
B, D, F	IPR027287	Glycoprotein E, immunoglobulin-like domain, flavivirus	Domain
B, D, F	IPR014412	Genome polyprotein, Flavivirus	Family
B, D, F	IPR036253	Flavivirus glycoprotein, central and dimerisation domain superfamily	Homologous Superfamily
B, D, F	IPR011492	Non-structural protein NS3-like, DEAD-box helicase, flavivirus	Domain
B, D, F	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
B, D, F	IPR026490	mRNA cap 0/1 methyltransferase	Domain
B, D, F	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
B, D, F	IPR001650	Helicase, C-terminal domain-like	Domain
B, D, F	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
B, D, F	IPR013755	Flaviviral glycoprotein E, central domain, subdomain 1	Homologous Superfamily
B, D, F	IPR000752	Flavivirus non-structural protein NS2A	Domain
B, D, F	IPR047530	RNA-dependent RNA polymerase, flavivirus	Domain
B, D, F	IPR049486	Flavivridae NS3 helicase, C-terminal helical domain	Domain
B, D, F	IPR046811	RNA-directed RNA polymerase, thumb subdomain, flavivirus	Domain
B, D, F	IPR038055	Flaviviral glycoprotein E, dimerisation domain	Homologous Superfamily
B, D, F	IPR002877	Ribosomal RNA methyltransferase, FtsJ domain	Domain
B, D, F	IPR038302	Envelope glycoprotein M superfamily, flavivirus	Homologous Superfamily
B, D, F	IPR000069	Envelope glycoprotein M, flavivirus	Domain
B, D, F	IPR038345	Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily	Homologous Superfamily
B, D, F	IPR038688	Flavivirus polyprotein propeptide superfamily	Homologous Superfamily
B, D, F	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
B, D, F	IPR026470	Flavivirus envelope glycoprotein E, Stem/Anchor domain	Domain
B, D, F	IPR011998	Envelope glycoprotein E, central and dimerisation domain, flavivirus	Domain
B, D, F	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
B, D, F	IPR037172	Flavivirus capsid protein C superfamily	Homologous Superfamily
B, D, F	IPR000404	Flavivirus non-structural protein NS4A	Domain
B, D, F	IPR000487	Non-structural protein NS2B, flavivirus	Domain
B, D, F	IPR001528	Flavivirus non-structural protein NS4B	Domain
B, D, F	IPR001157	Non-structural protein NS1, flavivirus	Domain
B, D, F	IPR013756	Flaviviral glycoprotein E, central domain, subdomain 2	Homologous Superfamily
B, D, F	IPR001850	Non-structural protein NS3, peptidase S7, flavivirus	Domain
B, D, F	IPR000336	Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily	Homologous Superfamily
B, D, F	IPR002535	Flavivirus polyprotein propeptide	Domain
B, D, F	IPR043504	Peptidase S1, PA clan, chymotrypsin-like fold	Homologous Superfamily
B, D, F	IPR007094	RNA-directed RNA polymerase, catalytic domain	Domain
A, C, E	IPR000208	RNA-directed RNA polymerase, fingers/palm subdomains, flavivirus	Domain
A, C, E	IPR014756	Immunoglobulin E-set	Homologous Superfamily
A, C, E	IPR001122	Capsid protein C, flavivirus	Domain
A, C, E	IPR027287	Glycoprotein E, immunoglobulin-like domain, flavivirus	Domain
A, C, E	IPR014412	Genome polyprotein, Flavivirus	Family
A, C, E	IPR036253	Flavivirus glycoprotein, central and dimerisation domain superfamily	Homologous Superfamily
A, C, E	IPR011492	Non-structural protein NS3-like, DEAD-box helicase, flavivirus	Domain
A, C, E	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, C, E	IPR026490	mRNA cap 0/1 methyltransferase	Domain
A, C, E	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
A, C, E	IPR001650	Helicase, C-terminal domain-like	Domain
A, C, E	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
A, C, E	IPR013755	Flaviviral glycoprotein E, central domain, subdomain 1	Homologous Superfamily
A, C, E	IPR000752	Flavivirus non-structural protein NS2A	Domain
A, C, E	IPR047530	RNA-dependent RNA polymerase, flavivirus	Domain
A, C, E	IPR049486	Flavivridae NS3 helicase, C-terminal helical domain	Domain
A, C, E	IPR046811	RNA-directed RNA polymerase, thumb subdomain, flavivirus	Domain
A, C, E	IPR038055	Flaviviral glycoprotein E, dimerisation domain	Homologous Superfamily
A, C, E	IPR002877	Ribosomal RNA methyltransferase, FtsJ domain	Domain
A, C, E	IPR038302	Envelope glycoprotein M superfamily, flavivirus	Homologous Superfamily
A, C, E	IPR000069	Envelope glycoprotein M, flavivirus	Domain
A, C, E	IPR038345	Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily	Homologous Superfamily
A, C, E	IPR038688	Flavivirus polyprotein propeptide superfamily	Homologous Superfamily
A, C, E	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A, C, E	IPR026470	Flavivirus envelope glycoprotein E, Stem/Anchor domain	Domain
A, C, E	IPR011998	Envelope glycoprotein E, central and dimerisation domain, flavivirus	Domain
A, C, E	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A, C, E	IPR037172	Flavivirus capsid protein C superfamily	Homologous Superfamily
A, C, E	IPR000404	Flavivirus non-structural protein NS4A	Domain
A, C, E	IPR000487	Non-structural protein NS2B, flavivirus	Domain
A, C, E	IPR001528	Flavivirus non-structural protein NS4B	Domain
A, C, E	IPR001157	Non-structural protein NS1, flavivirus	Domain
A, C, E	IPR013756	Flaviviral glycoprotein E, central domain, subdomain 2	Homologous Superfamily
A, C, E	IPR001850	Non-structural protein NS3, peptidase S7, flavivirus	Domain
A, C, E	IPR000336	Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily	Homologous Superfamily
A, C, E	IPR002535	Flavivirus polyprotein propeptide	Domain
A, C, E	IPR043504	Peptidase S1, PA clan, chymotrypsin-like fold	Homologous Superfamily
A, C, E	IPR007094	RNA-directed RNA polymerase, catalytic domain	Domain