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Basic information

Entry
Database: PDB / ID: 6qbj
TitleStructure determination of transmembrane- C-terminal fragment of UL49.5 protein from bovine herpesvirus 1 by NMR spectroscopy and molecular dynamics
ComponentsEnvelope glycoprotein N
KeywordsVIRAL PROTEIN / Bovine herpesvirus 1 (BHV-1) / UL49.5 viral protein / transmembrane protein
Function / homologyEnvelope glycoprotein N domain / Herpesvirus UL49.5 envelope/tegument protein / Envelope glycoprotein N / viral envelope / membrane / Envelope glycoprotein N
Function and homology information
Biological speciesBovine alphaherpesvirus 1
MethodSOLUTION NMR / molecular dynamics
AuthorsKarska, N. / Rodziewicz-Motowidlo, S.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science CentreUMO-2014/14/E/NZ6/00164 Poland
CitationJournal: Biochim Biophys Acta Biomembr / Year: 2019
Title: Structure determination of UL49.5 transmembrane protein from bovine herpesvirus 1 by NMR spectroscopy and molecular dynamics.
Authors: Karska, N. / Graul, M. / Sikorska, E. / Zhukov, I. / Slusarz, M.J. / Kasprzykowski, F. / Lipinska, A.D. / Rodziewicz-Motowidlo, S.
History
DepositionDec 21, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.3Nov 15, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2
Item: _citation.country / _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: Envelope glycoprotein N


Theoretical massNumber of molelcules
Total (without water)4,2161
Polymers4,2161
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area100 Å2
ΔGint0 kcal/mol
Surface area4030 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Envelope glycoprotein N / UL49.5 / Virion protein


Mass: 4215.985 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Bovine alphaherpesvirus 1 / References: UniProt: Q89806

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H TOCSY
121anisotropic12D 1H-1H NOESY
131isotropic12D DQF-COSY
141anisotropic12D 1H-1H ROESY

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Sample preparation

DetailsType: micelle
Contents: 2.7 mM TMC.BHV, 100 mM DPC, 0.01 mM acetic acid -d4, 90 % H2O, 10 % D2O, 50% H2O/50% D2O
Details: NMR experiments were performed using 100 mM DPC-d38 in water (90%:10% H2O:D2O).The peptide (TMC.BHV) concentration was 2.7 mM. The acetic acid -d4 concentration was 0.01mM.
Label: 1 / Solvent system: 50% H2O/50% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2.7 mMTMC.BHVnatural abundance1
100 mMDPCnatural abundance1
0.01 mMacetic acid -d4natural abundance1
90 %H2Onatural abundance1
10 %D2Onatural abundance1
Sample conditionsIonic strength: 0.05 mM / Label: 1 / pH: 5 / PH err: 0.05 / Pressure: 1 atm / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Agilent Uniform NMR System / Manufacturer: Agilent / Model: Uniform NMR System / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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