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- PDB-2lm7: NMR structure of the C-terminal domain of VP7 in membrane mimicki... -

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Basic information

Entry
Database: PDB / ID: 2lm7
TitleNMR structure of the C-terminal domain of VP7 in membrane mimicking micelles
ComponentsOuter capsid glycoprotein VP7
KeywordsVIRAL PROTEIN / alpha helix / amphipathic / perforating peptide
Function / homologyGlycoprotein VP7 / Glycoprotein VP7, domain 1 / Glycoprotein VP7, domain 2 / Glycoprotein VP7 / host cell endoplasmic reticulum lumen / T=13 icosahedral viral capsid / viral outer capsid / metal ion binding / Outer capsid glycoprotein VP7
Function and homology information
Biological speciesRotavirus A
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailslowest energy, model 1
AuthorsElaid, S. / Libersou, S. / Ouldali, M. / Morellet, N. / Lepault, J. / Bouaziz, S.
CitationJournal: To be Published
Title: NMR structure of the C-terminal domain of VP7 in membrane mimicking micelles
Authors: Elaid, S. / Libersou, S. / Ouldali, M. / Rhayyat, R. / Henry, C. / Morellet, N. / Lepault, J. / Bouaziz, S.
History
DepositionNov 23, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Database references / Experimental preparation
Category: database_2 / pdbx_database_related ...database_2 / pdbx_database_related / pdbx_nmr_sample_details / pdbx_nmr_spectrometer
Item: _pdbx_nmr_sample_details.contents / _pdbx_nmr_spectrometer.model
Revision 1.2May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Outer capsid glycoprotein VP7


Theoretical massNumber of molelcules
Total (without water)7,3411
Polymers7,3411
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)8 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Outer capsid glycoprotein VP7


Mass: 7341.409 Da / Num. of mol.: 1 / Fragment: UNP residues 266-326
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rotavirus A / Strain: isolate Human/Belgium/4106/2000 G3-P11[14] / References: UniProt: Q3ZK60

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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 DQF-COSY

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Sample preparation

DetailsContents: 1 mM VP7-61-1, 100 mM [U-100% 2H] DPC-2, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMVP7-61-11
100 mMDPC-2[U-100% 2H]1
Sample conditionsIonic strength: 0 / pH: 3 / Pressure: ambient / Temperature: 323 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
ARIA2.3Linge, O'Donoghue and Nilgesstructure solution
ARIA2.3Linge, O'Donoghue and Nilgesrefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1210 / NOE intraresidue total count: 879 / NOE long range total count: 0 / NOE medium range total count: 119 / NOE sequential total count: 212
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 8

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