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- PDB-5nhq: Nuclear Magnetic Resonance Structure of the Human Polyoma JC Viru... -

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Basic information

Entry
Database: PDB / ID: 5nhq
TitleNuclear Magnetic Resonance Structure of the Human Polyoma JC Virus Agnoprotein
ComponentsAgnoprotein
KeywordsVIRAL PROTEIN / Agnoprotein / dimer / oligomer / polyomavirus / JCV / SV40 / BKV / Merkel cell / DNA replication / progressive multifocal leukoencephalopathy / alpha-helix / intrinsically unstructured
Function / homology
Function and homology information


host cell rough endoplasmic reticulum membrane / host cell nuclear membrane / channel activity / monoatomic ion transmembrane transport / host cell plasma membrane / DNA binding / membrane
Similarity search - Function
Polyomavirus agnoprotein / Polyomavirus agnoprotein
Similarity search - Domain/homology
Biological speciesJC polyomavirus
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsCoric, P. / Saribas, A.S. / Abou-Gharbia, M. / Childers, W. / Condra, J. / White, M.K. / Safak, M. / Bouaziz, S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of HealthRO1NS090949 United States
Temple University Drug Discovery Initiative161398 United States
Citation
Journal: J. Cell. Biochem. / Year: 2017
Title: Nuclear Magnetic Resonance Structure of the Human Polyoma JC Virus Agnoprotein.
Authors: Coric, P. / Saribas, A.S. / Abou-Gharbia, M. / Childers, W. / Condra, J.H. / White, M.K. / Safak, M. / Bouaziz, S.
#1: Journal: J. Virol. / Year: 2014
Title: Nuclear magnetic resonance structure revealed that the human polyomavirus JC virus agnoprotein contains an alpha-helix encompassing the Leu/Ile/Phe-rich domain.
Authors: Coric, P. / Saribas, A.S. / Abou-Gharbia, M. / Childers, W. / White, M.K. / Bouaziz, S. / Safak, M.
History
DepositionMar 22, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 26, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.2Jan 31, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.4Oct 30, 2019Group: Data collection / Database references / Category: pdbx_database_related / pdbx_nmr_spectrometer / Item: _pdbx_nmr_spectrometer.model
Revision 1.5Jun 19, 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: Agnoprotein


Theoretical massNumber of molelcules
Total (without water)8,0961
Polymers8,0961
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7950 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)12 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Agnoprotein / Agno


Mass: 8096.414 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically synthetized full protein / Source: (synth.) JC polyomavirus / References: UniProt: P03086

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Experimental details

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Experiment

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

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Sample preparation

DetailsType: lyophilized powder
Contents: 0.2 mM no labelling agnoprotein, trifluoroethanol/water
Details: 30% TFE and 200 mM hNaCl ave been added to the solution. The concentration of the sample is 0.2 mM
Label: Full agnoprotein / Solvent system: trifluoroethanol/water
SampleConc.: 0.2 mM / Component: agnoprotein / Isotopic labeling: no labelling
Sample conditionsIonic strength: 200 mM NaCl mM / Label: 70/30 (v/v) H2O/TFE / pH: 3 / PH err: 0.2 / Pressure: pa Pa / Temperature: 313 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz / Details: cryoprobe

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Processing

NMR software
NameVersionDeveloperClassification
CNSVersion: 1.2 at patch level 1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CcpNmr Analysis2.4.0CCPNchemical shift assignment
TopSpin3.2Bruker Biospinprocessing
CcpNmr Analysis2.4CCPNpeak picking
CNSVersion: 1.2 at patch level 1Brunger, Adams, Clore, Gros, Nilges and Readstructure calculation
RefinementMethod: DGSA-distance geometry simulated annealing / 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: 12

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