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Yorodumi- PDB-2rq4: Refinement of RNA binding domain 3 in CUG triplet repeat RNA-bind... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2rq4 | ||||||
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Title | Refinement of RNA binding domain 3 in CUG triplet repeat RNA-binding protein 1 | ||||||
Components | CUG-BP- and ETR-3-like factor 1 | ||||||
Keywords | TRANSCRIPTION / RRM domain / RBD / Activator / Alternative splicing / Cytoplasm / mRNA processing / Nucleus / Phosphoprotein / RNA-binding / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information BRE binding / perinucleolar compartment / post-transcriptional gene silencing / regulatory ncRNA-mediated post-transcriptional gene silencing / mRNA splice site recognition / pre-mRNA binding / embryo development ending in birth or egg hatching / regulation of alternative mRNA splicing, via spliceosome / mRNA destabilization / regulation of RNA splicing ...BRE binding / perinucleolar compartment / post-transcriptional gene silencing / regulatory ncRNA-mediated post-transcriptional gene silencing / mRNA splice site recognition / pre-mRNA binding / embryo development ending in birth or egg hatching / regulation of alternative mRNA splicing, via spliceosome / mRNA destabilization / regulation of RNA splicing / germ cell development / mRNA regulatory element binding translation repressor activity / mRNA 3'-UTR binding / mRNA processing / cytoplasmic stress granule / regulation of inflammatory response / ribonucleoprotein complex / negative regulation of cell population proliferation / negative regulation of gene expression / mRNA binding / positive regulation of gene expression / RNA binding / nucleoplasm / membrane / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / DGSA-distance geometry simulated annealing | ||||||
Model details | fewest violations, model 1 | ||||||
Authors | Tsuda, K. / Kuwasako, K. / Takahashi, M. / Someya, T. / Inoue, M. / Terada, T. / Kobayashi, N. / Shirouzu, M. / Kigawa, T. / Guntert, P. ...Tsuda, K. / Kuwasako, K. / Takahashi, M. / Someya, T. / Inoue, M. / Terada, T. / Kobayashi, N. / Shirouzu, M. / Kigawa, T. / Guntert, P. / Muto, Y. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2009 Title: Structural basis for the sequence-specific RNA-recognition mechanism of human CUG-BP1 RRM3 Authors: Tsuda, K. / Kuwasako, K. / Takahashi, M. / Someya, T. / Inoue, M. / Terada, T. / Kobayashi, N. / Shirouzu, M. / Kigawa, T. / Tanaka, A. / Sugano, S. / Guntert, P. / Muto, Y. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2rq4.cif.gz | 657.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2rq4.ent.gz | 572.9 KB | Display | PDB format |
PDBx/mmJSON format | 2rq4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rq/2rq4 ftp://data.pdbj.org/pub/pdb/validation_reports/rq/2rq4 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 12264.778 Da / Num. of mol.: 1 / Fragment: RNA recognition motif Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CUGBP1 / Production host: E. coli-cell-free synthesis / References: UniProt: Q92879 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 1.37mM [U-100% 13C; U-100% 15N] protein, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O |
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Sample | Conc.: 1.37 mM / Component: protein / Isotopic labeling: [U-100% 13C; U-100% 15N] |
Sample conditions | Ionic strength: 120 / pH: 7.0 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz |
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-Processing
NMR software |
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Refinement | Method: DGSA-distance geometry simulated annealing / Software ordinal: 1 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: fewest violations | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 40 / Conformers submitted total number: 20 / Representative conformer: 1 |