4UTA

Crystal structure of dengue 2 virus envelope glycoprotein in complex with the Fab fragment of the broadly neutralizing human antibody EDE1 C8

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d4utaa2	All beta proteins	Immunoglobulin-like beta-sandwich	E set domains	automated matches	automated matches	(dengue virus type 2 ) [TaxId: 11060 ],	SCOPe (2.08)
A	d4utaa1	Membrane and cell surface proteins and peptides	Viral glycoprotein, central and dimerisation domains	Viral glycoprotein, central and dimerisation domains	automated matches	automated matches	(dengue virus type 2 ) [TaxId: 11060 ],	SCOPe (2.08)
A	d4utaa3	Artifacts	Tags	Tags	Tags	C-terminal Tags	(dengue virus type 2 ) [TaxId: 11060 ],	SCOPe (2.08)
B	d4utab2	All beta proteins	Immunoglobulin-like beta-sandwich	E set domains	automated matches	automated matches	(dengue virus type 2 ) [TaxId: 11060 ],	SCOPe (2.08)
B	d4utab1	Membrane and cell surface proteins and peptides	Viral glycoprotein, central and dimerisation domains	Viral glycoprotein, central and dimerisation domains	automated matches	automated matches	(dengue virus type 2 ) [TaxId: 11060 ],	SCOPe (2.08)
B	d4utab3	Artifacts	Tags	Tags	Tags	C-terminal Tags	(dengue virus type 2 ) [TaxId: 11060 ],	SCOPe (2.08)
E [auth L]	d4utal1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E [auth L]	d4utal2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F [auth M]	d4utam1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F [auth M]	d4utam2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Flavi_glycop_C	e4utaA1	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	e4utaA2	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)
B	Flavi_glycop_C	e4utaB1	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)
B	Flavi_glycoprot	e4utaB2	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)
D [auth I]	V-set_8	e4utaI2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
D [auth I]	C1-set_1	e4utaI1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
C [auth H]	V-set_8	e4utaH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
C [auth H]	C1-set_1	e4utaH2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
E [auth L]	C1-set_4	e4utaL1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
E [auth L]	V-set	e4utaL2	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)
F [auth M]	C1-set_4	e4utaM1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
F [auth M]	V-set	e4utaM2	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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)
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)
E [auth L]	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)

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]	EDE1 C8 Fab, anti-Dengue virus 2 envelope dimer epitope,	VH-CH1	Homo sapiens (human)	IGHV3-6403, IGHV3-6405, IGHV3-64D06, IGHJ601, IGHJ602, IGHG103	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202415-0)
E [auth L], F [auth M]	EDE1 C8 Fab, anti-Dengue virus 2 envelope dimer epitope,	L-KAPPA	Homo sapiens (human)	IGKV3-1101, IGKJ201, IGKC*01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202415-0)

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 (2024-04-19)
E [auth L], F [auth M]	Light Chain	IGKV3	Kappa	envelope glycoprotein e	SAbDab (2024-04-19)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00869	Flavivirus glycoprotein, central and dimerisation domains (Flavi_glycoprot)	Flavivirus glycoprotein, central and dimerisation domains	-	Domain
A, B	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
A, B	ENVELOPE GLYCOPROTEIN E	protein binding binding protein dimerization activity RNA binding double-stranded RNA binding organic cyclic compound binding nucleic acid binding passive transmembrane transporter activity monoatomic ion channel activity channel activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity peptidase activity protein binding binding protein dimerization activity RNA binding double-stranded RNA binding organic cyclic compound binding nucleic acid binding passive transmembrane transporter activity monoatomic ion channel activity channel activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity 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 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 catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid helicase activity RNA helicase activity ATP-dependent activity, acting on RNA ATP-dependent activity cation binding metal ion binding RNA methyltransferase activity O-methyltransferase activity transferase activity, transferring one-carbon groups mRNA (nucleoside-2'-O-)-methyltransferase activity transferase activity S-adenosylmethionine-dependent methyltransferase activity methyltransferase activity mRNA methyltransferase activity 5'-3' RNA polymerase activity RNA polymerase activity RNA-dependent RNA polymerase activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups mRNA 5'-cap (guanine-N7-)-methyltransferase activity N-methyltransferase activity structural molecule 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 transport of virus cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein complex oligomerization protein-containing complex assembly cellular component organization or biogenesis cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process nucleic acid biosynthetic process organic substance metabolic process viral genome replication biosynthetic process viral RNA genome replication organic cyclic compound biosynthetic process organic substance biosynthetic process metabolic process macromolecule metabolic process symbiont-mediated perturbation of host cellular process 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 modulation of process of another organism symbiont-mediated perturbation of host defense response response to host defenses symbiont-mediated suppression of host JAK-STAT cascade 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 JAK-STAT cascade via inhibition of host TYK2 activity modulation by symbiont of host process catabolic process regulation of cellular process autophagy positive regulation of biological process modulation by virus of host process positive regulation of cellular metabolic process regulation of autophagy cellular catabolic process positive regulation of metabolic process induction by virus of host autophagy process utilizing autophagic mechanism positive regulation of cellular process modulation by virus of host cellular process positive regulation of autophagy regulation of biological process modulation by virus of host autophagy biological regulation regulation of cellular metabolic process regulation of catabolic process symbiont-mediated perturbation of host autophagy positive regulation of catabolic process regulation of cellular catabolic process positive regulation of cellular catabolic process regulation of metabolic process symbiont-mediated suppression of host type I interferon-mediated signaling pathway symbiont-mediated suppression of host interferon-mediated signaling pathway 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 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 suppression of cytoplasmic pattern recognition receptor signaling pathway organonitrogen compound metabolic process proteolysis protein metabolic process	membrane cellular anatomical entity virion component virion membrane extracellular region host intracellular membrane-bounded organelle host cellular component host intracellular part host cell endoplasmic reticulum host cell membrane host cell cytoplasm part host intracellular organelle host cell cytoplasm host cell part membrane cellular anatomical entity virion component virion membrane extracellular region host intracellular membrane-bounded organelle host cellular component host intracellular part host cell endoplasmic reticulum host cell membrane 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 host cell mitochondrion viral capsid host cell nucleus
C [auth H], D [auth I]	BROADLY NEUTRALIZING HUMAN ANTIBODY EDE1 C8 HEAVY CHAIN	-	-	-
E [auth L], F [auth M]	BROADLY NEUTRALIZING HUMAN ANTIBODY EDE1 C8 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
A, B	IPR000208	RNA-directed RNA polymerase, fingers/palm subdomains, flavivirus	Domain
A, B	IPR014756	Immunoglobulin E-set	Homologous Superfamily
A, B	IPR001122	Capsid protein C, flavivirus	Domain
A, B	IPR027287	Glycoprotein E, immunoglobulin-like domain, flavivirus	Domain
A, B	IPR014412	Genome polyprotein, Flavivirus	Family
A, B	IPR036253	Flavivirus glycoprotein, central and dimerisation domain superfamily	Homologous Superfamily
A, B	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B	IPR026490	mRNA cap 0/1 methyltransferase	Domain
A, B	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
A, B	IPR001650	Helicase, C-terminal domain-like	Domain
A, B	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
A, B	IPR013755	Flaviviral glycoprotein E, central domain, subdomain 1	Homologous Superfamily
A, B	IPR000752	Flavivirus non-structural protein NS2A	Domain
A, B	IPR047530	RNA-dependent RNA polymerase, flavivirus	Domain
A, B	IPR049486	Flavivridae NS3 helicase, C-terminal helical domain	Domain
A, B	IPR046811	RNA-directed RNA polymerase, thumb subdomain, flavivirus	Domain
A, B	IPR038055	Flaviviral glycoprotein E, dimerisation domain	Homologous Superfamily
A, B	IPR002877	Ribosomal RNA methyltransferase, FtsJ domain	Domain
A, B	IPR038302	Envelope glycoprotein M superfamily, flavivirus	Homologous Superfamily
A, B	IPR000069	Envelope glycoprotein M, flavivirus	Domain
A, B	IPR011492	Non-structural protein NS3-like, DEAD box helicase, flavivirus	Domain
A, B	IPR038345	Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily	Homologous Superfamily
A, B	IPR038688	Flavivirus polyprotein propeptide superfamily	Homologous Superfamily
A, B	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A, B	IPR026470	Flavivirus envelope glycoprotein E, Stem/Anchor domain	Domain
A, B	IPR011998	Envelope glycoprotein E, central and dimerisation domain, flavivirus	Domain
A, B	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A, B	IPR037172	Flavivirus capsid protein C superfamily	Homologous Superfamily
A, B	IPR000404	Flavivirus non-structural protein NS4A	Domain
A, B	IPR000487	Non-structural protein NS2B, flavivirus	Domain
A, B	IPR001528	Flavivirus non-structural protein NS4B	Domain
A, B	IPR001157	Non-structural protein NS1, flavivirus	Domain
A, B	IPR013756	Flaviviral glycoprotein E, central domain, subdomain 2	Homologous Superfamily
A, B	IPR001850	Non-structural protein NS3, peptidase S7, flavivirus	Domain
A, B	IPR000336	Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily	Homologous Superfamily
A, B	IPR002535	Flavivirus polyprotein propeptide	Domain
A, B	IPR043504	Peptidase S1, PA clan, chymotrypsin-like fold	Homologous Superfamily
A, B	IPR007094	RNA-directed RNA polymerase, catalytic domain	Domain