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Yorodumi- PDB-2dnl: Solution structure of RNA binding domain in Cytoplasmic polyadeny... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dnl | ||||||
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Title | Solution structure of RNA binding domain in Cytoplasmic polyadenylation element binding protein 3 | ||||||
Components | cytoplasmic polyadenylation element binding protein 3 | ||||||
Keywords | TRANSLATION / 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 negative regulation of cytoplasmic translational elongation / : / CCR4-NOT complex / regulation of dendritic spine development / 3'-UTR-mediated mRNA destabilization / translation factor activity, RNA binding / apical dendrite / mRNA 3'-UTR AU-rich region binding / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / positive regulation of dendritic spine development ...negative regulation of cytoplasmic translational elongation / : / CCR4-NOT complex / regulation of dendritic spine development / 3'-UTR-mediated mRNA destabilization / translation factor activity, RNA binding / apical dendrite / mRNA 3'-UTR AU-rich region binding / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / positive regulation of dendritic spine development / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / negative regulation of cytoplasmic translation / long-term memory / mRNA regulatory element binding translation repressor activity / mRNA 3'-UTR binding / positive regulation of translation / cellular response to amino acid stimulus / regulation of synaptic plasticity / RNA stem-loop binding / ribosome binding / midbody / postsynaptic density / negative regulation of translation / neuron projection / synapse / dendrite / negative regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics,restrained molecular dynamics | ||||||
Authors | Tsuda, K. / Nagata, T. / 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 in Cytoplasmic polyadenylation element binding protein 3 Authors: Tsuda, K. / Nagata, T. / 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 | 2dnl.cif.gz | 665.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dnl.ent.gz | 557.2 KB | Display | PDB format |
PDBx/mmJSON format | 2dnl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dn/2dnl ftp://data.pdbj.org/pub/pdb/validation_reports/dn/2dnl | 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: 12428.833 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: CPEB3 / Plasmid: P050719-10 / Production host: Cell free synthesis / References: UniProt: Q5T390, UniProt: Q8NE35*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: 1.06mM 13C-15N PROTEIN, 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: 120mM / pH: 7 / 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 |