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- PDB-1cwx: SOLUTION STRUCTURE OF THE HEPATITIS C VIRUS N-TERMINAL CAPSID PRO... -

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Basic information

Entry
Database: PDB / ID: 1cwx
TitleSOLUTION STRUCTURE OF THE HEPATITIS C VIRUS N-TERMINAL CAPSID PROTEIN 2-45 [C-HCV(2-45)]
ComponentsHEPATITIS C VIRUS CAPSID PROTEIN
KeywordsVIRAL PROTEIN / HELIX-LOOP-HELIX
Function / homology
Function and homology information


positive regulation of hexokinase activity / modulation by virus of host cellular process / translocation of peptides or proteins into host cell cytoplasm / Toll-like receptor 2 binding / viral capsid assembly / adhesion receptor-mediated virion attachment to host cell / TBC/RABGAPs / hepacivirin / host cell mitochondrial membrane / host cell lipid droplet ...positive regulation of hexokinase activity / modulation by virus of host cellular process / translocation of peptides or proteins into host cell cytoplasm / Toll-like receptor 2 binding / viral capsid assembly / adhesion receptor-mediated virion attachment to host cell / TBC/RABGAPs / hepacivirin / host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated suppression of host TRAF-mediated signal transduction / transformation of host cell by virus / positive regulation of cytokinesis / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / negative regulation of protein secretion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / endoplasmic reticulum-Golgi intermediate compartment membrane / SH3 domain binding / kinase binding / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / clathrin-dependent endocytosis of virus by host cell / viral nucleocapsid / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / entry receptor-mediated virion attachment to host cell / RNA helicase activity / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / RNA helicase / induction by virus of host autophagy / ribonucleoprotein complex / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding
Similarity search - Function
Hepatitis C Virus Capsid Protein; Chain A / Hepatitis C Virus Capsid Protein; Chain A / Hepatitis C virus core protein, chain A superfamily / Hepatitus C virus, Non-structural 5a protein, C-terminal / Hepatitis C virus NS5A, 1B domain superfamily / Hepatitis C virus non-structural protein NS2, C-terminal domain / Hepatitis C virus non-structural protein NS2, N-terminal domain / Hepatitis C virus non-structural protein NS2 / HCV NS5a protein C-terminal region / Hepatitis C virus, Non-structural protein NS4b ...Hepatitis C Virus Capsid Protein; Chain A / Hepatitis C Virus Capsid Protein; Chain A / Hepatitis C virus core protein, chain A superfamily / Hepatitus C virus, Non-structural 5a protein, C-terminal / Hepatitis C virus NS5A, 1B domain superfamily / Hepatitis C virus non-structural protein NS2, C-terminal domain / Hepatitis C virus non-structural protein NS2, N-terminal domain / Hepatitis C virus non-structural protein NS2 / HCV NS5a protein C-terminal region / Hepatitis C virus, Non-structural protein NS4b / Hepatitis C virus, Core protein, N-terminal / Hepatitis C virus non-structural protein NS4b / Hepatitis C virus capsid protein / Hepatitis C virus, Non-structural protein NS2 / Hepatitis C virus, Non-structural 5a protein / Hepatitis C virus, Non-structural 5a protein, domain 1a / Hepatitis C virus non-structural 5a, 1B domain / NS5A domain 1a superfamily / Hepatitis C virus non-structural 5a protein membrane anchor / Hepatitis C virus non-structural 5a zinc finger domain / Hepatitis C virus non-structural 5a domain 1b / Hepacivirus nonstructural protein 2 (NS2) protease domain profile. / Hepatitis C virus, Non-structural protein NS4a / Hepatitis C virus non-structural protein NS4a / Hepatitis C virus, Core protein, C-terminal / Hepatitis C virus core protein / Hepatitis C virus, Non-structural protein E2/NS1 / Hepatitis C virus non-structural protein E2/NS1 / Hepatitis C virus, Envelope glycoprotein E1 / Hepatitis C virus envelope glycoprotein E1 / RNA dependent RNA polymerase, hepatitis C virus / Viral RNA dependent RNA polymerase / Hepatitis C virus, NS3 protease, Peptidase S29 / Hepatitis C virus NS3 protease / Hepacivirus/Pegivirus NS3 protease domain profile. / DEAD box, Flavivirus / Flavivirus DEAD domain / Few Secondary Structures / Irregular / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
MethodSOLUTION NMR / DISTANCE GEOMETRY SIMULATED ANNEALING, MOLECULAR DYNAMICS MATRIX RELAXATION
AuthorsLadaviere, L. / Deleage, G. / Montserret, R. / Dalbon, P. / Jolivet, M. / Penin, F.
CitationJournal: To be Published
Title: Structural Analysis of the Immunodominant Antigenic Region of the Hepatitis C Virus Capsid Protein by NMR
Authors: Ladaviere, L. / Deleage, G. / Montserret, R. / Dalbon, P. / Jolivet, M. / Penin, F.
History
DepositionAug 27, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HEPATITIS C VIRUS CAPSID PROTEIN


Theoretical massNumber of molelcules
Total (without water)4,9101
Polymers4,9101
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)4 / 50MOST CONVERGENT STRUCTURES AT THE LEVEL OF BOTH HELICES. NOTE THAT 23 STRUCTURES OVER 50 HAD NO RESTRAINT VIOLATION > 0.5 ANGSTROM.
RepresentativeModel #4closest to the average

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Components

#1: Protein/peptide HEPATITIS C VIRUS CAPSID PROTEIN


Mass: 4909.684 Da / Num. of mol.: 1 / Fragment: N-TERMINAL FRAGMENT / Source method: obtained synthetically
Details: THE PROTEIN WAS CHEMICALLY SYNTHESIZED. THIS SEQUENCE OCCURS NATURALLY IN HEPATITIS C VIRUS (GENOTYPE 1A ISOLATE H77)..
References: UniProt: P27958

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121DQF-COSY
1312D ROESY
1412D TOCSY
NMR detailsText: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D HOMONUCLEAR TECHNIQUES.

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Sample preparation

DetailsContents: 40% D2-TRIFLUOROETHANOL;0.01M SODIUM PHOSPHATE;0.1M NACL
Sample conditionsIonic strength: 0.1M NACL / pH: 5.9 / Pressure: AMBIENT / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR5.1VARIANcollection
VNMR5.1VARIANdata analysis
X-PLOR3.1BRUNGERrefinement
X-PLOR3.1BRUNGERstructure solution
RefinementMethod: DISTANCE GEOMETRY SIMULATED ANNEALING, MOLECULAR DYNAMICS MATRIX RELAXATION
Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: MOST CONVERGENT STRUCTURES AT THE LEVEL OF BOTH HELICES. NOTE THAT 23 STRUCTURES OVER 50 HAD NO RESTRAINT VIOLATION > 0.5 ANGSTROM.
Conformers calculated total number: 50 / Conformers submitted total number: 4

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