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- PDB-1wj6: Solution structure of RSGI RUH-024, a PB1 domain in human cDNA, K... -

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Basic information

Entry
Database: PDB / ID: 1wj6
TitleSolution structure of RSGI RUH-024, a PB1 domain in human cDNA, KIAA0049
ComponentsKIAA0049 protein
KeywordsPROTEIN BINDING / PB1 domain / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


regulation of bone mineralization / phagophore assembly site / M band / peroxisomal membrane / mitogen-activated protein kinase binding / regulation of stress-activated MAPK cascade / autophagosome / negative regulation of osteoblast differentiation / Pexophagy / ubiquitin binding ...regulation of bone mineralization / phagophore assembly site / M band / peroxisomal membrane / mitogen-activated protein kinase binding / regulation of stress-activated MAPK cascade / autophagosome / negative regulation of osteoblast differentiation / Pexophagy / ubiquitin binding / macroautophagy / mitochondrial intermembrane space / late endosome / lysosome / nuclear body / receptor complex / intracellular membrane-bounded organelle / zinc ion binding / nucleoplasm / membrane / cytosol
Similarity search - Function
NBR1, PB1 domain / Next to BRCA1, central domain / Ig-like domain from next to BRCA1 gene / PB1 domain / PB1 domain / PB1 domain profile. / PB1 domain / Zinc finger ZZ-type signature. / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Zinc finger, ZZ type ...NBR1, PB1 domain / Next to BRCA1, central domain / Ig-like domain from next to BRCA1 gene / PB1 domain / PB1 domain / PB1 domain profile. / PB1 domain / Zinc finger ZZ-type signature. / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Zinc finger, ZZ type / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Roll / Immunoglobulin-like fold / Alpha Beta
Similarity search - Domain/homology
Next to BRCA1 gene 1 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsHamada, T. / Hirota, H. / Hayashi, F. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of RSGI RUH-024, a PB1 domain in human cDNA, KIAA0049
Authors: Hamada, T. / Hirota, H. / Hayashi, F. / Yokoyama, S.
History
DepositionMay 29, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 29, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 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_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 / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: KIAA0049 protein


Theoretical massNumber of molelcules
Total (without water)11,0571
Polymers11,0571
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 / 100structures with the least restraint violations, structures with the lowest energy, target function
RepresentativeModel #1lowest energy

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Components

#1: Protein KIAA0049 protein / RSGI RUH-024


Mass: 11057.033 Da / Num. of mol.: 1 / Fragment: PB1 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: KIAA0049 / Plasmid: P040114-25 / References: UniProt: Q14596

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
NMR detailsText: This structure was determined using 3D NMR techniques

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Sample preparation

DetailsContents: 1.15mM PB1 domain U-15N,13C; 20mM Tris-HCl buffer (pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 100mM NaCl / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA9001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1cVariancollection
NMRPipe21_2Delaglio, F.collection
NMRView5.0.4Johnson, B. A.data analysis
KUJIRA0.8995Kobayashi, N.structure solution
CYANA1.0.8Guentert, P.structure solution
CYANA1.0.8Guentert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations, structures with the lowest energy, target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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