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- PDB-1uh6: Solution Structure of the murine ubiquitin-like 5 protein from RI... -

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Basic information

Entry
Database: PDB / ID: 1uh6
TitleSolution Structure of the murine ubiquitin-like 5 protein from RIKEN cDNA 0610031K06
Componentsubiquitin-like 5
KeywordsStructural genomics / unknown function / beta-grasp fold / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


cellular protein modification process / protein tag / mRNA splicing, via spliceosome / nucleus / cytoplasm
Ubiquitin-like domain superfamily / Ubiquitin domain / Ubiquitin-like modifier Hub1/Ubl5 / Ubiquitin family
Ubiquitin-like protein 5
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsHayashi, F. / Shirouzu, M. / Terada, T. / Kigawa, T. / Inoue, M. / Yabuki, T. / Aoki, M. / Seki, E. / Matsuda, T. / Hirota, H. / Yoshida, M. / Tanaka, A. / Osanai, T. / Arakawa, T. / Carninci, P. / Kawai, J. / Hayashizaki, Y. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution Structure of the murine ubiquitin-like 5 protein from RIKEN cDNA 0610031K06
Authors: Hayashi, F. / Shirouzu, M. / Terada, T. / Kigawa, T. / Inoue, M. / Yabuki, T. / Aoki, M. / Seki, E. / Matsuda, T. / Hirota, H. / Yoshida, M. / Tanaka, A. / Osanai, T. / Arakawa, T. / Carninci, P. / Kawai, J. / Hayashizaki, Y. / Yokoyama, S.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJun 25, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ubiquitin-like 5


Theoretical massNumber of molelcules
Total (without water)11,3111
Polymers11,3111
Non-polymers00
Water0
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/peptide ubiquitin-like 5


Mass: 11310.926 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 / Gene: RIKEN cDNA 0610031K06 / Plasmid: 011010-5 / References: UniProt: Q9EPV8

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment

Conditions-ID: 1 / Solution-ID: 1

Experiment-IDType
13D 13C-separated NOESY
23D 15N-separated NOESY

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Sample preparation

DetailsContents: 0.5mM 13C, 15N-labeled protein; 20mM phosphate buffer; 500mM NaCl; 4mM DTT; 0.4mM NaN3; 8% D2O
Solvent system: 92% H2O, 8% D2O
Sample conditionsIonic strength: 520mM / pH: 6.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVariancollection
NMRPipe20020425Delaglio, F.processing
NMRView5.0.4Johnson, B. A.data analysis
Kujira0.816Kobayashi, 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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