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- PDB-2mj2: Structure of the dimerization domain of the human polyoma, JC vir... -

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Basic information

Entry
Database: PDB / ID: 2mj2
TitleStructure of the dimerization domain of the human polyoma, JC virus agnoprotein is an amphipathic alpha-helix.
ComponentsAgnoprotein
KeywordsVIRAL PROTEIN / Agnoprotein / polyomavirus JCV / DNA replication / progressive multifocal leukoencephalopathy
Function / homology
Function and homology information


host cell rough endoplasmic reticulum membrane / host cell nuclear membrane / protein complex oligomerization / monoatomic ion channel activity / 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
Model detailslowest energy, model 1
AuthorsCoric, P. / Saribas, S.A. / Abou-Gharbia, M. / Childers, W. / White, M. / Bouaziz, S. / Safak, M.
Citation
Journal: J.Virol. / Year: 2014
Title: The structure of the dimerization domain of the human polyoma, JC virus agnoprotein is an amphipathic alpha-helix
Authors: Coric, P. / Saribas, S.A. / Abou-Gharbia, M. / Childers, W. / White, M. / Bouaziz, S. / Safak, M.
#1: Journal: Virology / Year: 2013
Title: Essential roles of Leu/Ile/Phe-rich domain of JC virus agnoprotein in dimer/oligomer formation, protein stability and splicing of viral transcripts.
Authors: Sami Saribas, A. / Abou-Gharbia, M. / Childers, W. / Sariyer, I.K. / White, M.K. / Safak, M.
#2: Journal: Virology / Year: 2011
Title: Human polyomavirus JC small regulatory agnoprotein forms highly stable dimers and oligomers: implications for their roles in agnoprotein function.
Authors: Saribas, A.S. / Arachea, B.T. / White, M.K. / Viola, R.E. / Safak, M.
History
DepositionDec 23, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 23, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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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)4,2081
Polymers4,2081
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)17 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Agnoprotein / Agno


Mass: 4207.873 Da / Num. of mol.: 1 / Fragment: UNP residues 17-52 / Source method: obtained synthetically / 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-IDType
1112D 1H-1H NOESY
1212D 1H-1H TOCSY
1312D DQF-COSY
2412D 1H-1H NOESY
2512D 1H-1H TOCSY
2612D DQF-COSY
3712D 1H-1H NOESY
3812D 1H-1H TOCSY
3912D DQF-COSY

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Sample preparation

DetailsContents: 0.5 mM AGNO, 70 v/v H2O, 30 v/v [U-100% 2H] TFE, water with 30% (v/v) TFE (Trifluoroethanol, CF3CH2OH)
Solvent system: water with 30% (v/v) TFE (Trifluoroethanol, CF3CH2OH)
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMAGNO-11
70 v/vH2O-21
30 v/vTFE-3[U-100% 2H]1
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1no salts 3.0 ambient 293 K
2no salts 3.0 ambient 303 K
3no salts 3.0 ambient 313 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
TopSpin1.3Bruker Biospincollection
CcpNmr Analysis2.2.2CCPNchemical shift assignment
CcpNmr Analysis2.2.2CCPNdata analysis
CcpNmr Analysis2.2.2CCPNpeak picking
ARIA2.3.1Linge, O'Donoghue and Nilgesgeometry optimization
ARIA2.3.1Linge, O'Donoghue and Nilgesrefinement
ARIA2.3.1Linge, O'Donoghue and Nilgesstructure solution
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: 17

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