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- PDB-1v9j: Solution structure of a BolA-like protein from Mus musculus -

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Basic information

Entry
Database: PDB / ID: 1v9j
TitleSolution structure of a BolA-like protein from Mus musculus
ComponentsBolA-like protein RIKEN cDNA 1110025L05
Keywordsstructural genomics / unknown function / Stationary phase morphogene / stress-induced morphogene / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


protein maturation by iron-sulfur cluster transfer / [2Fe-2S] cluster assembly / iron-sulfur cluster binding / intracellular iron ion homeostasis / nucleus / cytosol / cytoplasm
Similarity search - Function
BolA protein / BolA-like superfamily / BolA-like protein / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / Simulated annealing, Torsion angle dynamics
AuthorsKasai, T. / Inoue, M. / Koshiba, S. / Yabuki, T. / Aoki, M. / Nunokawa, E. / Seki, E. / Matsuda, T. / Matsuda, N. / Tomo, Y. ...Kasai, T. / Inoue, M. / Koshiba, S. / Yabuki, T. / Aoki, M. / Nunokawa, E. / Seki, E. / Matsuda, T. / Matsuda, N. / Tomo, Y. / Shirouzu, M. / Terada, T. / Obayashi, N. / Hamana, H. / Shinya, N. / Tatsuguchi, A. / Yasuda, S. / Yoshida, M. / Hirota, H. / Matsuo, Y. / Tani, K. / Suzuki, H. / Arakawa, T. / Carninci, P. / Kawai, J. / Hayashizaki, Y. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Protein Sci. / Year: 2004
Title: Solution structure of a BolA-like protein from Mus musculus
Authors: Kasai, T. / Inoue, M. / Koshiba, S. / Yabuki, T. / Aoki, M. / Nunokawa, E. / Seki, E. / Matsuda, T. / Matsuda, N. / Tomo, Y. / Shirouzu, M. / Terada, T. / Obayashi, N. / Hamana, H. / Shinya, ...Authors: Kasai, T. / Inoue, M. / Koshiba, S. / Yabuki, T. / Aoki, M. / Nunokawa, E. / Seki, E. / Matsuda, T. / Matsuda, N. / Tomo, Y. / Shirouzu, M. / Terada, T. / Obayashi, N. / Hamana, H. / Shinya, N. / Tatsuguchi, A. / Yasuda, S. / Yoshida, M. / Hirota, H. / Matsuo, Y. / Tani, K. / Suzuki, H. / Arakawa, T. / Carninci, P. / Kawai, J. / Hayashizaki, Y. / Kigawa, T. / Yokoyama, S.
History
DepositionJan 26, 2004Deposition site: PDBJ / Processing site: PDBJ
SupersessionFeb 10, 2004ID: 1IW5
Revision 1.0Feb 10, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BolA-like protein RIKEN cDNA 1110025L05


Theoretical massNumber of molelcules
Total (without water)12,9821
Polymers12,9821
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)20 / 200target function
RepresentativeModel #1lowest energy

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Components

#1: Protein BolA-like protein RIKEN cDNA 1110025L05


Mass: 12981.577 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: CELL-FREE PROTEIN SYNTHESIS / Plasmid: P011101-17 / References: UniProt: Q8BGS2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy. The first 27 Residues are derived from the purification tag sequence.

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Sample preparation

DetailsContents: 1.2MM U-13C, 15N BOLA-LIKE PROTEIN; 50MM SODIUM PHOSPHATE BUFFER, 100MM SODIUM CHLORIDE, 0.02% SODIUM AZIDE, 1MM D-DTT; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 100mM / pH: 6.0 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe1.8Delagliodata analysis
CNS1refinement
RefinementMethod: Simulated annealing, Torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20

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