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Yorodumi- PDB-2dgu: Solution structure of the RNA binding domain in Heterogeneous nuc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dgu | ||||||
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Title | Solution structure of the RNA binding domain in Heterogeneous nuclear ribonucleoprotein Q | ||||||
Components | Heterogeneous nuclear ribonucleoprotein Q | ||||||
Keywords | RNA BINDING PROTEIN / RRM domain / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information mRNA editing complex / CRD-mediated mRNA stability complex / mRNA modification / negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / mCRD-mediated mRNA stability complex / : / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / CRD-mediated mRNA stabilization / histone pre-mRNA 3'end processing complex / positive regulation of cytoplasmic translation ...mRNA editing complex / CRD-mediated mRNA stability complex / mRNA modification / negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / mCRD-mediated mRNA stability complex / : / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / CRD-mediated mRNA stabilization / histone pre-mRNA 3'end processing complex / positive regulation of cytoplasmic translation / GAIT complex / RNA processing / catalytic step 2 spliceosome / RNA splicing / mRNA 5'-UTR binding / mRNA splicing, via spliceosome / osteoblast differentiation / cellular response to type II interferon / negative regulation of translation / ribonucleoprotein complex / endoplasmic reticulum / RNA binding / nucleoplasm / membrane / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics, restrained molecular dynamics | ||||||
Authors | Abe, C. / Muto, Y. / Inoue, M. / Kigawa, T. / Terada, T. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution structure of the RNA binding domain in Heterogeneous nuclear ribonucleoprotein Q Authors: Abe, C. / Muto, Y. / Inoue, M. / Kigawa, T. / Terada, T. / Shirouzu, M. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dgu.cif.gz | 624 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dgu.ent.gz | 544.5 KB | Display | PDB format |
PDBx/mmJSON format | 2dgu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dg/2dgu ftp://data.pdbj.org/pub/pdb/validation_reports/dg/2dgu | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 11422.991 Da / Num. of mol.: 1 / Fragment: RNA recognition motif Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: SYNCRIP / Plasmid: P051017-06 / Production host: Cell free synthesis / References: UniProt: O60506 |
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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: 20mM d-Tris-HCl(pH7.0), 100mM NaCl, 1mM d-DTT, 0.02% NaN3, 10% D2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 100mM / pH: 7.0 / Pressure: ambient / Temperature: 298 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: torsion angle dynamics, restrained molecular dynamics Software ordinal: 1 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function, structures with the lowest energy, structures with the least restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 20 |