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- PDB-2kvl: NMR structure of the C-terminal domain of VP7 -

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Basic information

Entry
Database: PDB / ID: 2kvl
TitleNMR structure of the C-terminal domain of VP7
ComponentsMajor outer capsid protein VP7
KeywordsVIRAL PROTEIN / Capsid protein / Host endoplasmic reticulum / Virion / C terminal domain / membrane destabilisation
Function / homology
Function and homology information


host cell endoplasmic reticulum lumen / T=13 icosahedral viral capsid / viral outer capsid / membrane => GO:0016020 / metal ion binding
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1600 / Glycoprotein VP7 / Glycoprotein VP7, domain 1 / Glycoprotein VP7, domain 2 / Glycoprotein VP7 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special
Similarity search - Domain/homology
Outer capsid glycoprotein VP7
Similarity search - Component
Biological speciesHuman rotavirus A
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsElaid, S. / Libersou, S. / Lepault, J. / Morellet, N. / Bouaziz, S.
CitationJournal: To be Published
Title: NMR structure of the C-terminal domain of VP7
Authors: Elaid, S. / Libersou, S. / Lepault, J. / Morellet, N. / Bouaziz, S.
History
DepositionMar 17, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 30, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Major outer capsid protein VP7


Theoretical massNumber of molelcules
Total (without water)7,3411
Polymers7,3411
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)10 / 100structures with the lowest energy
RepresentativeModel #1minimized average

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Components

#1: Protein Major outer capsid protein VP7


Mass: 7341.409 Da / Num. of mol.: 1 / Fragment: C-terminal domain / Source method: obtained synthetically
Details: The peptide synthesized by automated solid phase using Fmoc strategy and purified by reverse phase HPLC
Source: (synth.) Human rotavirus A / References: UniProt: Q6SKR8

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1212D 1H-1H TOCSY
1312D 1H-1H COSY

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Sample preparation

DetailsContents: 1 mM VP7 Cter domain, 1 v/v CD3OH/CDCl3 methanol/chloroform, CDCl3/CD3OH
Solvent system: CDCl3/CD3OH
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMVP7 Cter domain1
1 v/vmethanol/chloroformCD3OH/CDCl31
Sample conditionsPressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAvance6001
Bruker AvanceBrukerAvance6002

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Processing

NMR software
NameVersionDeveloperClassification
Sparky3.113Goddardchemical shift assignment
Sparky3.113Goddardpeak picking
TOPSPIN1.3Bruker Biospinprocessing
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 765 / NOE intraresidue total count: 363 / NOE long range total count: 0 / NOE medium range total count: 145 / NOE sequential total count: 159 / Hydrogen bond constraints total count: 2
NMR representativeSelection criteria: minimized average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10 / Maximum lower distance constraint violation: 0 Å / Maximum upper distance constraint violation: 0 Å
NMR ensemble rmsDistance rms dev: 0.00127 Å / Distance rms dev error: 5.8E-5 Å

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