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- PDB-2cp8: Solution structure of the RSGI RUH-046, a UBA domain from human N... -

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Basic information

Entry
Database: PDB / ID: 2cp8
TitleSolution structure of the RSGI RUH-046, a UBA domain from human Next to BRCA1 gene 1 protein (KIAA0049 protein) R923H variant
ComponentsNext to BRCA1 gene 1 protein
KeywordsPROTEIN BINDING / UBA domain / structural genomics / human / NPPSFA / National Project on Protein Structural and Functional Analyses / 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 / Ubiquitin-associated (UBA) domain / Zinc finger ZZ-type signature. / Zinc-binding domain, present in Dystrophin, CREB-binding protein. ...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 / Ubiquitin-associated (UBA) 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 / Helicase, Ruva Protein; domain 3 / Immunoglobulin-like fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Next to BRCA1 gene 1 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated anneling, torsion angle dynamics
AuthorsOhashi, W. / Hirota, H. / Yamazaki, T. / Muto, Y. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the RSGI RUH-046, a UBA domain from human Next to BRCA1 gene 1 protein (KIAA0049 protein) R923H variant
Authors: Ohashi, W. / Hirota, H. / Yamazaki, T. / Muto, Y. / Yokoyama, S.
History
DepositionMay 19, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Next to BRCA1 gene 1 protein


Theoretical massNumber of molelcules
Total (without water)5,8261
Polymers5,8261
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 / 100target function
RepresentativeModel #1lowest target function

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Components

#1: Protein Next to BRCA1 gene 1 protein / KIAA0049 protein / Neighbor of BRCA1 gene 1 protein


Mass: 5825.658 Da / Num. of mol.: 1 / Fragment: UBA
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free (E.Coli) / Plasmid: P040719-07 / 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: The structure was determined using triple-resonance NMR spectroscopy

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Sample preparation

DetailsContents: 2.62mM RSGI RUH-046 U-13C, 15N; 20mM Tris-HCl U-2H, 100mM NaCl, 1mM DTT U-2H, 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

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.1Brukercollection
NMRPipe2.1Delaglioprocessing
NMRView5.0.4Johnsondata analysis
KUJIRA0.9295Kobayashidata analysis
CYANA2.0.17Guntertstructure solution
CYANA2.0.17Guntertrefinement
RefinementMethod: simulated anneling, torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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