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Yorodumi- PDB-2rqc: Solution Structure of RNA-binding domain 3 of CUGBP1 in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2rqc | ||||||
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Title | Solution Structure of RNA-binding domain 3 of CUGBP1 in complex with RNA (UG)3 | ||||||
Components |
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Keywords | TRANSCRIPTION/RNA / RRM DOMAIN / RBD / PROTEIN-RNA COMPLEX / TRANSCRIPTION-RNA COMPLEX / STRUCTURAL GENOMICS / NPPSFA / NATIONAL PROJECT ON PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES / RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE / RSGI / ACTIVATOR / ALTERNATIVE SPLICING / CYTOPLASM / MRNA PROCESSING / NUCLEUS / PHOSPHOPROTEIN / RNA-BINDING | ||||||
Function / homology | Function and homology information BRE binding / perinucleolar compartment / post-transcriptional gene silencing / mRNA splice site recognition / regulatory ncRNA-mediated post-transcriptional gene silencing / pre-mRNA binding / embryo development ending in birth or egg hatching / regulation of alternative mRNA splicing, via spliceosome / mRNA destabilization / germ cell development ...BRE binding / perinucleolar compartment / post-transcriptional gene silencing / mRNA splice site recognition / regulatory ncRNA-mediated post-transcriptional gene silencing / pre-mRNA binding / embryo development ending in birth or egg hatching / regulation of alternative mRNA splicing, via spliceosome / mRNA destabilization / germ cell development / regulation of RNA splicing / mRNA regulatory element binding translation repressor activity / mRNA 3'-UTR binding / cytoplasmic stress granule / mRNA processing / 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, restrained MOLECULAR DYNAMICS, SIMULATED ANNEALING, ENERGY MINIMIZATION | ||||||
Model details | fewest violations, model 1 | ||||||
Authors | Tsuda, K. / Kuwasako, K. / Takahashi, M. / Someya, T. / Muto, Y. / Inoue, M. / Kigawa, T. / Terada, T. / Shirouzu, M. / 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 | 2rqc.cif.gz | 739.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2rqc.ent.gz | 618.9 KB | Display | PDB format |
PDBx/mmJSON format | 2rqc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2rqc_validation.pdf.gz | 382 KB | Display | wwPDB validaton report |
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Full document | 2rqc_full_validation.pdf.gz | 571.6 KB | Display | |
Data in XML | 2rqc_validation.xml.gz | 32.4 KB | Display | |
Data in CIF | 2rqc_validation.cif.gz | 61.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rq/2rqc ftp://data.pdbj.org/pub/pdb/validation_reports/rq/2rqc | HTTPS FTP |
-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, RESIDUES 383-484 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: E. COLI - CELL-FREE PROTEIN SYNTHESIS / Gene: CUGBP1 / Production host: FREE PROTEIN SYNTHESIS / References: UniProt: Q92879 |
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#2: RNA chain | Mass: 1909.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: RNA WAS PREPARED BY IN VITRO TRANSCRIPTION |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions | Ionic strength: 100 / pH: 7 / Pressure: AMBIENT / Temperature: 288 K |
-NMR measurement
NMR spectrometer | Type: BRUKER AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz |
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-Processing
NMR software |
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Refinement | Method: DGSA-distance geometry simulated annealing, restrained MOLECULAR DYNAMICS, SIMULATED ANNEALING, ENERGY MINIMIZATION Software ordinal: 1 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: fewest violations | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1 |