7JTF

Structure of Hepatitis C Virus Envelope Glycoprotein E2 core from genotype 6a bound to broadly neutralizing antibody RM2-01

External Resource: Annotation

Domain Annotation: ECOD Classification
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	C1-set_1	e7jtfA2	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)
A	V-set_12	e7jtfA1	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)
D [auth C]	C1-set_1	e7jtfC2	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)
D [auth C]	V-set_12	e7jtfC1	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)
B	C1-set_4	e7jtfB2	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	e7jtfB1	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)
E [auth D]	C1-set_4	e7jtfD1	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 D]	V-set	e7jtfD2	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	HCV_NS1	e7jtfF1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: HCV envelope glycoprotein E2 (From Topology)	T: HCV envelope glycoprotein E2	F: HCV_NS1	ECOD (1.6)
C [auth E]	HCV_NS1	e7jtfE1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: HCV envelope glycoprotein E2 (From Topology)	T: HCV envelope glycoprotein E2	F: HCV_NS1	ECOD (1.6)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A, D [auth C]	Heavy Chain	IGHV1	-	envelope glycoprotein e2	SAbDab (2024-09-13)
B, E [auth D]	Light Chain	IGKV1	Kappa	envelope glycoprotein e2	SAbDab (2024-09-13)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, D [auth C]	RM2-01 Fab heavy chain	-	-	-
B, E [auth D]	RM2-01 Fab light chain	-	-	-
C [auth E], F	Envelope glycoprotein E2	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 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 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 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 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 structural molecule activity cation binding transition metal ion binding zinc ion binding metal ion binding	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 nucleic acid biosynthetic process viral genome replication biosynthetic process viral RNA genome replication viral process metabolic process macromolecule metabolic 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 response to host defenses response to stimulus response to other organism response to defenses of other organism modulation by virus of host process response to external stimulus virus-mediated perturbation of host defense response response to biotic stimulus response to host response to external biotic stimulus modulation by virus of host cellular process catabolic process regulation of cellular process autophagy positive regulation of biological 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 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 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 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 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 symbiont-mediated perturbation of host immune response symbiont-mediated perturbation of host defenses 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 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	host cellular component host intracellular part host cell cytoplasm host cell part host cell lipid droplet host intracellular region cellular anatomical entity 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 host cell cytoplasm host cell part host cell lipid droplet host intracellular region cellular anatomical entity 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 intracellular anatomical structure cytoplasm host cell endoplasmic reticulum host cell endomembrane system host cell endoplasmic reticulum membrane viral nucleocapsid viral capsid virion component cell periphery plasma membrane membrane host cell plasma membrane host cell perinuclear region of cytoplasm virion membrane lipid droplet intracellular organelle organelle intracellular non-membrane-bounded organelle non-membrane-bounded organelle host cell nucleus viral membrane viral envelope protein-containing complex ribonucleoprotein complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth E], F	IPR002522	Hepatitis C virus, Core protein, N-terminal	Domain
C [auth E], F	IPR043128	Reverse transcriptase/Diguanylate cyclase domain	Homologous Superfamily
C [auth E], F	IPR038568	Hepatitis C virus NS5A, 1B domain superfamily	Homologous Superfamily
C [auth E], F	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
C [auth E], F	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
C [auth E], F	IPR001650	Helicase, C-terminal domain-like	Domain
C [auth E], F	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
C [auth E], F	IPR002868	Hepatitis C virus, Non-structural 5a protein	Domain
C [auth E], F	IPR038170	NS5A domain 1a superfamily	Homologous Superfamily
C [auth E], F	IPR002518	Hepatitis C virus, Non-structural protein NS2	Domain
C [auth E], F	IPR013192	Hepatitis C virus, Non-structural 5a protein, domain 1a	Domain
C [auth E], F	IPR002521	Hepatitis C virus, Core protein, C-terminal	Domain
C [auth E], F	IPR042209	Hepatitis C virus non-structural protein NS2, N-terminal domain	Homologous Superfamily
C [auth E], F	IPR000745	Hepatitis C virus, Non-structural protein NS4a	Domain
C [auth E], F	IPR011492	Non-structural protein NS3-like, DEAD box helicase, flavivirus	Domain
C [auth E], F	IPR042205	Hepatitis C virus non-structural protein NS2, C-terminal domain	Homologous Superfamily
C [auth E], F	IPR002166	RNA dependent RNA polymerase, hepatitis C virus	Family
C [auth E], F	IPR002519	Hepatitis C virus, Envelope glycoprotein E1	Domain
C [auth E], F	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
C [auth E], F	IPR044896	Hepatitis C virus core protein, chain A superfamily	Homologous Superfamily
C [auth E], F	IPR024350	Hepatitus C virus, Non-structural 5a protein, C-terminal	Domain
C [auth E], F	IPR013193	Hepatitis C virus non-structural 5a, 1B domain	Domain
C [auth E], F	IPR004109	Hepatitis C virus, NS3 protease	Domain
C [auth E], F	IPR049913	Hepatitis C virus, p7 channel	Domain
C [auth E], F	IPR002531	Hepatitis C virus, Non-structural protein E2/NS1	Domain
C [auth E], F	IPR043504	Peptidase S1, PA clan, chymotrypsin-like fold	Homologous Superfamily
C [auth E], F	IPR007094	RNA-directed RNA polymerase, catalytic domain	Domain
C [auth E], F	IPR001490	Hepatitis C virus, Non-structural protein NS4b	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 R01GM133198.

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7JTF

Structure of Hepatitis C Virus Envelope Glycoprotein E2 core from genotype 6a bound to broadly neutralizing antibody RM2-01

External Resource: Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

SAbDab Antibody Annotation SAbDab Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage