4C2I

Cryo-EM structure of Dengue virus serotype 1 complexed with Fab fragments of human antibody 1F4

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)
A	PF02832	e4c2iA1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF02832	ECOD (1.6)
A	PF00869	e4c2iA2	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: PF00869	ECOD (1.6)
A	PF21659	e4c2iA3	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: PF21659	ECOD (1.6)
C	PF02832	e4c2iC1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF02832	ECOD (1.6)
C	PF00869	e4c2iC2	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: PF00869	ECOD (1.6)
C	PF21659	e4c2iC3	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: PF21659	ECOD (1.6)
E	PF02832	e4c2iE1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF02832	ECOD (1.6)
E	PF00869	e4c2iE2	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: PF00869	ECOD (1.6)
E	PF21659	e4c2iE3	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: PF21659	ECOD (1.6)
B	PF01004	e4c2iB1	A: extended segments	X: Small envelope protein M (From Topology)	H: Small envelope protein M (From Topology)	T: Small envelope protein M	F: PF01004	ECOD (1.6)
D	PF01004	e4c2iD1	A: extended segments	X: Small envelope protein M (From Topology)	H: Small envelope protein M (From Topology)	T: Small envelope protein M	F: PF01004	ECOD (1.6)
F	PF01004	e4c2iF1	A: extended segments	X: Small envelope protein M (From Topology)	H: Small envelope protein M (From Topology)	T: Small envelope protein M	F: PF01004	ECOD (1.6)
G [auth H]	PF07654	e4c2iH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
G [auth H]	PF07686	e4c2iH2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
I [auth M]	PF07654	e4c2iM1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
I [auth M]	PF07686	e4c2iM2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
H [auth L]	PF07654	e4c2iL1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
H [auth L]	PF07686	e4c2iL2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
J [auth N]	PF07654	e4c2iN1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
J [auth N]	PF07686	e4c2iN2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	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
G [auth H], I [auth M]	1F4 Fab	VH-CH1	Homo sapiens (human)	IGHV3-3301, IGHV3-3304, IGHJ601, IGHJ602, IGHG101, IGHG102, IGHG104, IGHG105	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_LAMBDA	IMGT (202416-0)
H [auth L], J [auth N]	1F4 Fab	L-LAMBDA	Homo sapiens (human)	IGLV1-3601, IGLJ201, IGLJ301, IGLC201, IGLC202, IGLC304	V-DOMAIN V-LAMBDA, C-DOMAIN C-LAMBDA	IG	FAB-GAMMA-1_LAMBDA	IMGT (202416-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
G [auth H], I [auth M]	Heavy Chain	IGHV3	-	envelope protein	SAbDab (2024-04-26)
H [auth L], J [auth N]	Light Chain	IGLV1	Lambda	envelope protein	SAbDab (2024-04-26)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
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
B, D, F	PF01004	Flavivirus envelope glycoprotein M (Flavi_M)	Flavivirus envelope glycoprotein M	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C, E	ENVELOPE PROTEIN	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 transport of virus	membrane cellular anatomical entity virion component virion membrane 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 membrane cellular anatomical entity virion component virion membrane 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
B, D, F	POLYPROTEIN	RNA binding double-stranded RNA binding 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 RNA binding double-stranded RNA binding 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 protein binding protein dimerization 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	cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein complex oligomerization protein-containing complex assembly cellular process cellular component organization or biogenesis cellular biosynthetic process cellular metabolic process RNA metabolic process viral life cycle primary metabolic process nucleobase-containing compound biosynthetic process cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein complex oligomerization protein-containing complex assembly cellular process cellular component organization or biogenesis cellular biosynthetic process cellular 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 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 viral process organic substance biosynthetic process metabolic process macromolecule metabolic process symbiont-mediated perturbation of host cellular process biological process involved in interspecies interaction between organisms response to stimulus response to biotic stimulus biological process involved in symbiotic interaction 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 biological process involved in interaction with host 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 fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell 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 transport of virus 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 virion attachment to host cell adhesion of symbiont to host cell adhesion of symbiont to host organonitrogen compound metabolic process proteolysis protein metabolic process	membrane cellular anatomical entity host intracellular membrane-bounded organelle host cellular component host intracellular part host cell cytoplasm host cell part host intracellular region host cell mitochondrion host cell cytoplasm part host intracellular organelle host cell endoplasmic reticulum host cell membrane host cell endomembrane system membrane cellular anatomical entity host intracellular membrane-bounded organelle host cellular component host intracellular part host cell cytoplasm host cell part host intracellular region host cell mitochondrion host cell cytoplasm part host intracellular organelle host cell endoplasmic reticulum host cell membrane host cell endomembrane system host cell endoplasmic reticulum membrane viral capsid virion component virion membrane extracellular region viral membrane viral envelope
G [auth H], I [auth M]	HEAVY CHAIN FAB FRAGMENT OF ANTIBODY 1F4	-	-	-
H [auth L], J [auth N]	LIGHT CHAIN FAB FRAGMENT OF ANTIBODY 1F4	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, E	IPR038345	Flavivirus envelope glycoprotein E, Stem/Anchor domain 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	IPR013755	Flaviviral glycoprotein E, central domain, subdomain 1	Homologous Superfamily
A, C, E	IPR038055	Flaviviral glycoprotein E, dimerisation domain	Homologous Superfamily
A, C, E	IPR014756	Immunoglobulin E-set	Homologous Superfamily
A, C, E	IPR027287	Glycoprotein E, immunoglobulin-like domain, flavivirus	Domain
A, C, E	IPR013756	Flaviviral glycoprotein E, central domain, subdomain 2	Homologous Superfamily
A, C, E	IPR000336	Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily	Homologous Superfamily
A, C, E	IPR036253	Flavivirus glycoprotein, central and dimerisation domain superfamily	Homologous Superfamily
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	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	IPR011492	Non-structural protein NS3-like, DEAD box helicase, 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