4JZN

Three dimensional structure of broadly neutralizing human anti - Hepatitis C virus (HCV) glycoprotein E2 Fab fragment HC84-1

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)
A	V-set_8	e4jznA4	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)
A	C1-set_1	e4jznA3	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	V-set_8	e4jznC4	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	C1-set_1	e4jznC3	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 I]	V-set_8	e4jznI4	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)
E [auth I]	C1-set_1	e4jznI3	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)
B	C1-set_4	e4jznB4	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)
B	V-set_3	e4jznB3	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_3	ECOD (1.6)
D	C1-set_4	e4jznD4	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)
D	V-set_3	e4jznD3	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_3	ECOD (1.6)
G [auth P]	C1-set_4	e4jznP4	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)
G [auth P]	V-set_3	e4jznP3	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_3	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
E [auth I]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
G [auth P]	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
A, C, E [auth I]	E2, neutralizing	VH-CH1	Homo sapiens (human)	IGHV1-6901, IGHV1-6912, IGHV1-6913, IGHV1-69D01, IGHJ401, IGHJ402, IGHJ403, IGHG101, IGHG102, IGHG104	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_V-LAMBDA-C-KAPPA	IMGT (202450-0)
B, D, G [auth P]	E2, neutralizing	V-LAMBDA-C-KAPPA	Homo sapiens (human)	IGLV3-2103, IGLJ201, IGLJ302, IGLJ301, IGKC*01	V-DOMAIN V-LAMBDA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_V-LAMBDA-C-KAPPA	IMGT (202450-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A, C, E [auth I]	Heavy Chain	IGHV1	-	envelope glycoprotein e2	SAbDab (2024-12-20)
B, D, G [auth P]	Light Chain	IGLV3	Lambda	envelope glycoprotein e2	SAbDab (2024-12-20)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C, E [auth I]	Anti-HCV E2 Fab HC84-1 heavy chain	-	-	-
B, D, G [auth P]	Anti-HCV E2 Fab HC84-1 light chain	-	-	-
F [auth K]	Envelope glycoprotein E2	protein binding binding Toll-like receptor 2 binding signaling receptor binding Toll-like receptor binding 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 SH3 domain binding protein binding binding Toll-like receptor 2 binding signaling receptor binding Toll-like receptor binding 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 SH3 domain binding protein domain specific binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding 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 5'-3' RNA polymerase activity RNA polymerase activity transferase activity RNA-dependent RNA polymerase activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups cysteine-type peptidase activity cysteine-type endopeptidase activity RNA binding nucleic acid binding kinase binding enzyme binding pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity, acting on acid anhydrides passive transmembrane transporter activity channel activity transporter activity transmembrane transporter activity structural molecule activity cation binding transition metal ion binding zinc ion binding metal ion binding	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 negative regulation of protein transport protein localization regulation of localization establishment of protein localization cellular localization nitrogen compound transport regulation of cellular process regulation of protein localization transport negative regulation of biological process negative regulation of transport protein localization to extracellular region localization negative regulation of secretion regulation of secretion by cell secretion by cell cellular macromolecule localization negative regulation of cellular process negative regulation of secretion by cell negative regulation of protein localization regulation of biological process regulation of transport secretion biological regulation regulation of establishment of protein localization establishment of protein localization to extracellular region negative regulation of establishment of protein localization export from cell regulation of protein transport protein secretion establishment of localization regulation of secretion regulation of protein secretion negative regulation of protein secretion protein transport regulation of cellular localization macromolecule localization regulation of cytokinesis positive regulation of cell division regulation of cell cycle process positive regulation of biological process cytokinesis positive regulation of cell cycle regulation of cell division positive regulation of cytokinesis positive regulation of cell cycle process cell division cell cycle regulation of cell cycle positive regulation of cellular process cell cycle process symbiont-mediated perturbation of host cellular process biological process involved in interspecies interaction between organisms symbiont-mediated suppression of host JAK-STAT cascade 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 JAK-STAT cascade via inhibition of STAT activity symbiont-mediated perturbation of host process symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity symbiont-mediated perturbation of host signal transduction pathway modulation of process of another organism symbiont-mediated suppression of host TRAF-mediated signal transduction apoptotic process cell death programmed cell death symbiont-mediated perturbation of host defense response modulation by virus of host process virus-mediated perturbation of host defense response modulation by virus of host cellular process catabolic process autophagy regulation of autophagy positive regulation of metabolic process induction by virus of host autophagy process utilizing autophagic mechanism positive regulation of autophagy modulation by virus of host autophagy regulation of catabolic process positive regulation of catabolic process regulation of metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process regulation of macromolecule metabolic process gene expression regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process symbiont-mediated suppression of host interferon-mediated signaling pathway symbiont-mediated suppression of host type I interferon-mediated signaling pathway fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell virion assembly viral capsid assembly import into cell receptor-mediated endocytosis of virus by host cell vesicle-mediated transport 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 translocation of peptides or proteins into host translocation of molecules into host translocation of peptides or proteins into host cell cytoplasm viral gene expression viral translational frameshifting viral translation transmembrane transport monoatomic ion transmembrane transport monoatomic ion transport positive regulation of phosphorylation regulation of catalytic activity regulation of transferase activity positive regulation of phosphate metabolic process positive regulation of molecular function regulation of phosphate metabolic process phosphate-containing compound metabolic process phosphorus metabolic process positive regulation of hexokinase activity positive regulation of transferase activity positive regulation of phosphorus metabolic process phosphorylation positive regulation of catalytic activity regulation of molecular function positive regulation of kinase activity regulation of kinase activity regulation of hexokinase activity regulation of phosphorylation regulation of phosphorus metabolic process virion attachment to host cell receptor-mediated virion attachment to host cell adhesion of symbiont to host cell adhesion of symbiont to host adhesion receptor-mediated virion attachment to host cell symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity response to stimulus symbiont-mediated suppression of host pathogen-associated molecular pattern receptor signaling pathway response to biotic stimulus symbiont-mediated suppression of host immune response symbiont-mediated suppression of host innate immune response symbiont-mediated suppression of host defenses symbiont-mediated perturbation of host innate immune response response to host response to external biotic stimulus response to host defenses response to other organism symbiont-mediated perturbation of host immune response symbiont-mediated perturbation of host defenses response to defenses of other organism response to external stimulus symbiont-mediated suppression of cytoplasmic pattern recognition receptor signaling pathway transformation of host cell by virus proteolysis protein metabolic process symbiont-mediated perturbation of host cell cycle progression symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint entry receptor-mediated virion attachment to host cell	host cellular component host intracellular part cellular anatomical structure host cell cytoplasm host cell part host cell lipid droplet host intracellular region host cell cytoplasm part host intracellular membrane-bounded organelle host cell membrane host cell mitochondrion host intracellular organelle host cell mitochondrial envelope host cell mitochondrial membrane host cellular component host intracellular part cellular anatomical structure host cell cytoplasm host cell part host cell lipid droplet host intracellular region host cell cytoplasm part host intracellular membrane-bounded organelle host cell membrane host cell mitochondrion host intracellular organelle host cell mitochondrial envelope host cell mitochondrial membrane membrane-bounded organelle intracellular anatomical structure membrane intracellular membrane-bounded organelle intracellular organelle bounding membrane of organelle organelle endoplasmic reticulum-Golgi intermediate compartment membrane endoplasmic reticulum-Golgi intermediate compartment cytoplasm organelle membrane host cell endoplasmic reticulum host cell endomembrane system host cell endoplasmic reticulum membrane viral nucleocapsid viral capsid virion component host cell plasma membrane host cell perinuclear region of cytoplasm virion membrane host cell nucleus viral membrane viral envelope protein-containing complex ribonucleoprotein complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
F [auth K]	IPR002522	Hepatitis C virus, Core protein, N-terminal	Domain
F [auth K]	IPR043128	Reverse transcriptase/Diguanylate cyclase domain	Homologous Superfamily
F [auth K]	IPR054175	NS3 RNA helicase, C-terminal helical domain	Domain
F [auth K]	IPR038568	Hepatitis C virus NS5A, 1B domain superfamily	Homologous Superfamily
F [auth K]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
F [auth K]	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
F [auth K]	IPR001650	Helicase, C-terminal domain-like	Domain
F [auth K]	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
F [auth K]	IPR002868	Hepatitis C virus, Non-structural 5a protein	Domain
F [auth K]	IPR038170	NS5A domain 1a superfamily	Homologous Superfamily
F [auth K]	IPR002518	Hepatitis C virus, Non-structural protein NS2	Domain
F [auth K]	IPR013192	Hepatitis C virus, Non-structural 5a protein, domain 1a	Domain
F [auth K]	IPR002521	Hepatitis C virus, Core protein, C-terminal	Domain
F [auth K]	IPR042209	Hepatitis C virus non-structural protein NS2, N-terminal domain	Homologous Superfamily
F [auth K]	IPR000745	Hepatitis C virus, Non-structural protein NS4a	Domain
F [auth K]	IPR011492	Non-structural protein NS3-like, DEAD box helicase, flavivirus	Domain
F [auth K]	IPR042205	Hepatitis C virus non-structural protein NS2, C-terminal domain	Homologous Superfamily
F [auth K]	IPR002166	RNA dependent RNA polymerase, hepatitis C virus	Family
F [auth K]	IPR002519	Hepatitis C virus, Envelope glycoprotein E1	Domain
F [auth K]	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
F [auth K]	IPR044896	Hepatitis C virus core protein, chain A superfamily	Homologous Superfamily
F [auth K]	IPR024350	Hepatitus C virus, Non-structural 5a protein, C-terminal	Domain
F [auth K]	IPR013193	Hepatitis C virus non-structural 5a, 1B domain	Domain
F [auth K]	IPR004109	Hepatitis C virus, NS3 protease	Domain
F [auth K]	IPR049913	Hepatitis C virus, p7 channel	Domain
F [auth K]	IPR002531	Hepatitis C virus, Non-structural protein E2/NS1	Domain
F [auth K]	IPR043504	Peptidase S1, PA clan, chymotrypsin-like fold	Homologous Superfamily
F [auth K]	IPR007094	RNA-directed RNA polymerase, catalytic domain	Domain
F [auth K]	IPR001490	Hepatitis C virus, Non-structural protein NS4b	Domain