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- PDB-2rrb: Refinement of RNA binding domain in human Tra2 beta protein -

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Basic information

Entry
Database: PDB / ID: 2rrb
TitleRefinement of RNA binding domain in human Tra2 beta protein
ComponentscDNA FLJ40872 fis, clone TUTER2000283, highly similar to Homo sapiens transformer-2-beta (SFRS10) gene
KeywordsRNA BINDING PROTEIN / RRM domain / RBD / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


cerebral cortex regionalization / embryonic brain development / pre-mRNA binding / RNA splicing, via transesterification reactions / positive regulation of mRNA splicing, via spliceosome / RHOBTB1 GTPase cycle / nuclear inner membrane / regulation of alternative mRNA splicing, via spliceosome / regulation of RNA splicing / Processing of Capped Intron-Containing Pre-mRNA ...cerebral cortex regionalization / embryonic brain development / pre-mRNA binding / RNA splicing, via transesterification reactions / positive regulation of mRNA splicing, via spliceosome / RHOBTB1 GTPase cycle / nuclear inner membrane / regulation of alternative mRNA splicing, via spliceosome / regulation of RNA splicing / Processing of Capped Intron-Containing Pre-mRNA / RHOBTB2 GTPase cycle / mRNA Splicing - Major Pathway / cellular response to glucose stimulus / spliceosomal complex / mRNA splicing, via spliceosome / protein domain specific binding / mRNA binding / protein-containing complex / RNA binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Transformer-2 protein homolog beta / cDNA FLJ40872 fis, clone TUTER2000283, highly similar to Homo sapiens transformer-2-beta (SFRS10) gene
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailsfewest violations, model 1
AuthorsTsuda, K. / Kuwasako, K. / Takahashi, M. / Someya, T. / Inoue, M. / Kigawa, T. / Terada, T. / Shirouzu, M. / Sugano, S. / Muto, Y. ...Tsuda, K. / Kuwasako, K. / Takahashi, M. / Someya, T. / Inoue, M. / Kigawa, T. / Terada, T. / Shirouzu, M. / Sugano, S. / Muto, Y. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Nucleic Acids Res. / Year: 2011
Title: Structural basis for the dual RNA-recognition modes of human Tra2-beta RRM.
Authors: Tsuda, K. / Someya, T. / Kuwasako, K. / Takahashi, M. / He, F. / Unzai, S. / Inoue, M. / Harada, T. / Watanabe, S. / Terada, T. / Kobayashi, N. / Shirouzu, M. / Kigawa, T. / Tanaka, A. / ...Authors: Tsuda, K. / Someya, T. / Kuwasako, K. / Takahashi, M. / He, F. / Unzai, S. / Inoue, M. / Harada, T. / Watanabe, S. / Terada, T. / Kobayashi, N. / Shirouzu, M. / Kigawa, T. / Tanaka, A. / Sugano, S. / Guntert, P. / Yokoyama, S. / Muto, Y.
History
DepositionJun 17, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Apr 27, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: cDNA FLJ40872 fis, clone TUTER2000283, highly similar to Homo sapiens transformer-2-beta (SFRS10) gene


Theoretical massNumber of molelcules
Total (without water)10,8911
Polymers10,8911
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 / 200structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein cDNA FLJ40872 fis, clone TUTER2000283, highly similar to Homo sapiens transformer-2-beta (SFRS10) gene


Mass: 10891.192 Da / Num. of mol.: 1 / Fragment: RNA recognition motif
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8N1H4, UniProt: P62995*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1213D 1H-13C NOESY

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Sample preparation

DetailsContents: 1 mM [U-100% 13C; U-100% 15N] Human transformer 2 beta-1, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: Human transformer 2 beta-1 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 100 / 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
AMBER9Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, Kollmrefinement
xwinnmr3.6Bruker Biospincollection
NMRPipe20060801Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRView5.0.4Johnson, One Moon Scientificdata analysis
Kujira0.9843N. Kobayashidata analysis
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1

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