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- PDB-2k47: Solution structure of the C-terminal N-RNA binding domain of the ... -

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Entry
Database: PDB / ID: 2k47
TitleSolution structure of the C-terminal N-RNA binding domain of the Vesicular Stomatitis Virus Phosphoprotein
ComponentsPhosphoprotein
KeywordsREPLICATION / flexible tail / Chaperone / Cytoplasm / Phosphoprotein / RNA replication / Virion
Function / homology
Function and homology information


RNA folding chaperone / viral transcription / viral genome replication / virion component / host cell cytoplasm / phosphorylation / RNA-dependent RNA polymerase activity
Similarity search - Function
Vesicular stomatitis virus phosphoprotein C-terminal domain / : / Vesiculovirus phosphoprotein / Phosphoprotein, central domain / Phosphoprotein, C-terminal domain, viral / Helicase, Ruva Protein; domain 3 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesVesicular stomatitis Indiana virus
MethodSOLUTION NMR / simulated annealing
AuthorsRibeiro, E.A. / Favier, A. / Gerard, F.C. / Leyrat, C. / Brutscher, B. / Blondel, D. / Ruigrok, R.W. / Blackledge, M. / Jamin, M.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Solution Structure of the C-Terminal Nucleoprotein-RNA Binding Domain of the Vesicular Stomatitis Virus Phosphoprotein.
Authors: Ribeiro, E.A. / Favier, A. / Gerard, F.C. / Leyrat, C. / Brutscher, B. / Blondel, D. / Ruigrok, R.W. / Blackledge, M. / Jamin, M.
History
DepositionMay 28, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Sep 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3May 29, 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: Phosphoprotein


Theoretical massNumber of molelcules
Total (without water)9,0931
Polymers9,0931
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)20 / 50020 structures for lowest energy
RepresentativeModel #1fewest violations

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Components

#1: Protein Phosphoprotein / / P protein / M1


Mass: 9093.418 Da / Num. of mol.: 1 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vesicular stomatitis Indiana virus / Gene: P / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03520

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HN(CA)CB
1214D HC(CCO)NH
1312D (HB)CB(CGCDCE)HE/(HB)CB(CGCD)HD
1413D 15N NOESY-HSQC
1513D aliphatic/aromatic 13C NOESY-HSQC
1613D methyl selective 13C NOESY-HSQC
1713D BEST HNCO/HN(CO)CA
181R1, R2(CPMG 1H-15N Het NOE
1913D BEST HNCO/HN(CO)CA

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Sample preparation

DetailsContents: 1.2 mM [U-100% 13C; U-100% 15N] protein, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 1.2 mM / Component: protein / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionspH: 7.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian InovaVarianINOVA6001
Varian INOVAVarianINOVA8002

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Processing

NMR softwareName: CNS / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Atnos-candid using CYANA, then CNS interfaced to the program Sculptor for rdc refinement
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: 20 structures for lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 20 / Representative conformer: 1

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