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- PDB-1v95: Solution Structure of Anticodon Binding Domain from Nuclear Recep... -

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Basic information

Entry
Database: PDB / ID: 1v95
TitleSolution Structure of Anticodon Binding Domain from Nuclear Receptor Coactivator 5 (Human KIAA1637 Protein)
ComponentsNuclear receptor coactivator 5
KeywordsRNA BINDING PROTEIN / Nuclear receptor coactivator 5 / Coactivator independent of AF-2 function (CIA) / Structural genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


regulation of signal transduction / negative regulation of insulin receptor signaling pathway / transcription corepressor activity / actin cytoskeleton / insulin receptor signaling pathway / glucose homeostasis / chromatin binding / negative regulation of transcription by RNA polymerase II / RNA binding / extracellular space / nucleoplasm
Similarity search - Function
: / Anticodon-binding domain / Anticodon-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Nuclear receptor coactivator 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsZhao, C. / Kigawa, T. / Tochio, N. / Koshiba, S. / Inoue, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution Structure of Anticodon Binding Domain from Nuclear Receptor Coactivator 5 (Human KIAA1637 Protein)
Authors: Zhao, C. / Kigawa, T. / Tochio, N. / Koshiba, S. / Inoue, M. / Yokoyama, S.
History
DepositionJan 20, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 20, 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_software ...database_2 / pdbx_nmr_software / 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_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nuclear receptor coactivator 5


Theoretical massNumber of molelcules
Total (without water)14,3151
Polymers14,3151
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)20 / 100structures with the least restraint violations, target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Nuclear receptor coactivator 5 / NCoA-5 / Coactivator independent of AF-2 / CIA


Mass: 14315.061 Da / Num. of mol.: 1 / Fragment: Anticodon Binding Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: KAZUSA cDNA fj00747s1 / Plasmid: P030506-92 / References: UniProt: Q9HCD5

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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

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Sample preparation

DetailsContents: 1.02mM Anticodon Binding Domain U-15N, 13C; 20mM d-Tris-HCl (pH7.5); 200mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O; 90% H2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 200mM / pH: 7.5 / Pressure: ambient / Temperature: 298.0 K

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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: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
NMRPipe20020425Delaglio, F.processing
NMRView5.0.4Johnson, B. A.data analysis
KUJIRA0.86Kobayashi, N.data analysis
CYANA1.0.7Guentert, P.structure solution
CYANA1.0.7Guentert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations, target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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