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- PDB-1r7f: NMR structure of the membrane anchor domain (1-31) of the nonstru... -

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Basic information

Entry
Database: PDB / ID: 1r7f
TitleNMR structure of the membrane anchor domain (1-31) of the nonstructural protein 5A (NS5A) of hepatitis C virus (Ensemble of 43 structures. Sample in 100mM SDS)
ComponentsGenome polyprotein
KeywordsMEMBRANE PROTEIN / Membrane anchor domain / HCV NS5A protein / peptide.
Function / homology
Function and homology information


Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen / oxylipin biosynthetic process / lipid oxidation / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / fatty acid biosynthetic process / metal ion binding / cytoplasm
Similarity search - Function
Lipoxygenase, plant / Lipoxygenase, domain 3 / Plant lipoxygenase, PLAT/LH2 domain / Lipoxygenase, conserved site / Lipoxygenases iron-binding region signature 2. / Lipoxygenase, iron binding site / Lipoxygenases iron-binding region signature 1. / Lipoxygenase / Lipoxygenase, C-terminal / Lipoxigenase, C-terminal domain superfamily ...Lipoxygenase, plant / Lipoxygenase, domain 3 / Plant lipoxygenase, PLAT/LH2 domain / Lipoxygenase, conserved site / Lipoxygenases iron-binding region signature 2. / Lipoxygenase, iron binding site / Lipoxygenases iron-binding region signature 1. / Lipoxygenase / Lipoxygenase, C-terminal / Lipoxigenase, C-terminal domain superfamily / Lipoxygenase / Lipoxygenase iron-binding catalytic domain profile. / Lipoxygenase homology 2 (beta barrel) domain / PLAT/LH2 domain / PLAT/LH2 domain superfamily / PLAT/LH2 domain / PLAT domain profile. / Hepatitis C virus non-structural 5a protein membrane anchor
Similarity search - Domain/homology
MethodSOLUTION NMR / distance geometry, simulated annealing, molecular dynamics, energy minimization
AuthorsPenin, F. / Brass, V. / Appel, N. / Ramboarina, S. / Montserret, R. / Ficheux, D. / Blum, H.E. / Bartenschlager, R. / Moradpour, D.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Structure and function of the membrane anchor domain of hepatitis C virus nonstructural protein 5A.
Authors: Penin, F. / Brass, V. / Appel, N. / Ramboarina, S. / Montserret, R. / Ficheux, D. / Blum, H.E. / Bartenschlager, R. / Moradpour, D.
History
DepositionOct 21, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Genome polyprotein


Theoretical massNumber of molelcules
Total (without water)3,7701
Polymers3,7701
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)43 / 100structures with the least restraint violations
Representative

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Components

#1: Protein/peptide Genome polyprotein


Mass: 3770.423 Da / Num. of mol.: 1
Fragment: Nonstructural protein NS5A (P56)(residues 1973-2003 of Swiss-Prot sequence P27958)
Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence is naturally found in hepatitis C virus.
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
1212D TOCSY
131DQF-COSY
1411H-13C HSQC

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Sample preparation

DetailsContents: 1.2mM NS5A[1-31], 10mM DTTd10 / Solvent system: 100mM SDS in H2O/D2O 95/5 (v/v)
Sample conditionspH: 6 / Pressure: ambient / Temperature: 313 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1Variancollection
VNMR6.1Varianprocessing
VNMR6.1Variandata analysis
X-PLOR3.85Brungerstructure solution
X-PLOR3.85Brungerrefinement
RefinementMethod: distance geometry, simulated annealing, molecular dynamics, energy minimization
Software ordinal: 1
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 43

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