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Yorodumi- PDB-2ytv: Solution structure of the fifth cold-shock domain of the human KI... -
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-Basic information
Entry | Database: PDB / ID: 2ytv | ||||||
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Title | Solution structure of the fifth cold-shock domain of the human KIAA0885 protein (unr protein) | ||||||
Components | Cold shock domain-containing protein E1 | ||||||
Keywords | RNA BINDING PROTEIN / CELL-FREE PROTEIN SYNTHESIS / BETA-BARREL / TRANSLATIONAL REGULATION / RNA CHAPERONE / RNA/DNA BINDING / QB FOLD / GREEK-KEY TOPOLOGY / UNR PROTEIN / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information CRD-mediated mRNA stability complex / nuclear-transcribed mRNA catabolic process, no-go decay / mCRD-mediated mRNA stability complex / RISC complex binding / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / CRD-mediated mRNA stabilization / IRES-dependent viral translational initiation / positive regulation of cytoplasmic translation / regulation of translational initiation / stress granule assembly ...CRD-mediated mRNA stability complex / nuclear-transcribed mRNA catabolic process, no-go decay / mCRD-mediated mRNA stability complex / RISC complex binding / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / CRD-mediated mRNA stabilization / IRES-dependent viral translational initiation / positive regulation of cytoplasmic translation / regulation of translational initiation / stress granule assembly / P-body / cytoplasmic stress granule / RNA stem-loop binding / male gonad development / Golgi apparatus / RNA binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Goroncy, A.K. / Tochio, N. / Tomizawa, T. / Koshiba, S. / Watanabe, S. / Harada, T. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: J.Struct.Funct.Genom. / Year: 2010 Title: The NMR solution structures of the five constituent cold-shock domains (CSD) of the human UNR (upstream of N-ras) protein. Authors: Goroncy, A.K. / Koshiba, S. / Tochio, N. / Tomizawa, T. / Inoue, M. / Watanabe, S. / Harada, T. / Tanaka, A. / Ohara, O. / Kigawa, T. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ytv.cif.gz | 456.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ytv.ent.gz | 386.3 KB | Display | PDB format |
PDBx/mmJSON format | 2ytv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yt/2ytv ftp://data.pdbj.org/pub/pdb/validation_reports/yt/2ytv | HTTPS FTP |
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-Related structure data
Related structure data | 1wfqC 1x65C 2ytxC 2ytyC C: citing same article (ref.) |
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Similar structure data | |
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: 8553.508 Da / Num. of mol.: 1 / Fragment: FIFTH COLD-SHOCK DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: CELL-FREE PROTEIN SYNTHESIS / Gene: KIAA0885 / Plasmid: P070129-03 / References: UniProt: O75534 |
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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: 0.79mM COLD-SHOCK DOMAIN, 20mM d-TRIS-HCL, 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: 120 mM / pH: 7 / Pressure: AMBIENT / Temperature: 296 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 / 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 |