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Yorodumi- PDB-2dnq: Solution structure of RNA binding domain 1 in RNA-binding protein 30 -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dnq | ||||||
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Title | Solution structure of RNA binding domain 1 in RNA-binding protein 30 | ||||||
Components | RNA-binding protein 4B | ||||||
Keywords | RNA 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 cap-independent translational initiation / IRES-dependent translational initiation of linear mRNA / pre-mRNA intronic pyrimidine-rich binding / circadian regulation of translation / negative regulation of translation in response to stress / regulation of nucleocytoplasmic transport / miRNA-mediated gene silencing by inhibition of translation / response to arsenic-containing substance / mRNA cis splicing, via spliceosome / miRNA binding ...cap-independent translational initiation / IRES-dependent translational initiation of linear mRNA / pre-mRNA intronic pyrimidine-rich binding / circadian regulation of translation / negative regulation of translation in response to stress / regulation of nucleocytoplasmic transport / miRNA-mediated gene silencing by inhibition of translation / response to arsenic-containing substance / mRNA cis splicing, via spliceosome / miRNA binding / positive regulation of muscle cell differentiation / regulation of alternative mRNA splicing, via spliceosome / entrainment of circadian clock by photoperiod / RNA processing / pre-mRNA intronic binding / negative regulation of translational initiation / cyclin binding / mRNA 3'-UTR binding / circadian regulation of gene expression / mRNA splicing, via spliceosome / cytoplasmic stress granule / circadian rhythm / Circadian Clock / regulation of translation / cell differentiation / negative regulation of translation / nuclear speck / mRNA binding / positive regulation of gene expression / nucleolus / protein-containing complex / RNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics, restrained molecular dynamics | ||||||
Authors | Tsuda, K. / 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 RNA binding domain 1 in RNA-binding protein 30 Authors: Tsuda, K. / 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 | 2dnq.cif.gz | 530.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dnq.ent.gz | 446.8 KB | Display | PDB format |
PDBx/mmJSON format | 2dnq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2dnq_validation.pdf.gz | 340.9 KB | Display | wwPDB validaton report |
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Full document | 2dnq_full_validation.pdf.gz | 465.6 KB | Display | |
Data in XML | 2dnq_validation.xml.gz | 32.8 KB | Display | |
Data in CIF | 2dnq_validation.cif.gz | 49.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dn/2dnq ftp://data.pdbj.org/pub/pdb/validation_reports/dn/2dnq | HTTPS FTP |
-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: 9820.983 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: RBM30 / Plasmid: P050704-15 / Production host: Cell free synthesis / References: UniProt: Q9BQ04, UniProt: Q9BWF3*PLUS |
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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: 1.17mM 13C-15N PROTEIN, 20mM d-Tris-HCl(pH7.0), 100mM NaCl, 1mM d-DTT, 0.02% NaN3; 90% H2O, 10% D2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 120mM / 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 |