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Yorodumi- PDB-5ytt: Crystal structure of YB1 cold-shock domain in complex with UCAUGU -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ytt | |||||||||
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Title | Crystal structure of YB1 cold-shock domain in complex with UCAUGU | |||||||||
Components |
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Keywords | RNA BINDING PROTEIN/RNA / YB1 / cold-shock domain / CAUG / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex | |||||||||
Function / homology | Function and homology information tRNA transport / CRD-mediated mRNA stability complex / C5-methylcytidine-containing RNA reader activity / miRNA transport / negative regulation of striated muscle cell differentiation / RNA transport / Noncanonical activation of NOTCH3 / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / messenger ribonucleoprotein complex / CRD-mediated mRNA stabilization ...tRNA transport / CRD-mediated mRNA stability complex / C5-methylcytidine-containing RNA reader activity / miRNA transport / negative regulation of striated muscle cell differentiation / RNA transport / Noncanonical activation of NOTCH3 / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / messenger ribonucleoprotein complex / CRD-mediated mRNA stabilization / protein localization to cytoplasmic stress granule / histone pre-mRNA 3'end processing complex / embryonic morphogenesis / U12-type spliceosomal complex / positive regulation of cytoplasmic translation / mRNA stabilization / cellular response to interleukin-7 / miRNA binding / mRNA Splicing - Minor Pathway / negative regulation of cellular senescence / Processing of Capped Intron-Containing Pre-mRNA / positive regulation of cell division / epidermis development / mRNA Splicing - Major Pathway / RNA splicing / P-body / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / mRNA processing / cytoplasmic stress granule / Interferon gamma signaling / sequence-specific double-stranded DNA binding / single-stranded DNA binding / GTPase binding / double-stranded DNA binding / regulation of gene expression / in utero embryonic development / negative regulation of translation / nucleic acid binding / ribonucleoprotein complex / mRNA binding / intracellular membrane-bounded organelle / synapse / chromatin binding / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | |||||||||
Authors | Yang, X. / Huang, Y. | |||||||||
Funding support | China, 2items
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Citation | Journal: J.Biol.Chem. / Year: 2019 Title: Crystal structure of a Y-box binding protein 1 (YB-1)-RNA complex reveals key features and residues interacting with RNA. Authors: Yang, X.J. / Zhu, H. / Mu, S.R. / Wei, W.J. / Yuan, X. / Wang, M. / Liu, Y. / Hui, J. / Huang, Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ytt.cif.gz | 57.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ytt.ent.gz | 38.3 KB | Display | PDB format |
PDBx/mmJSON format | 5ytt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yt/5ytt ftp://data.pdbj.org/pub/pdb/validation_reports/yt/5ytt | HTTPS FTP |
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-Related structure data
Related structure data | 5ytsC 5ytvC 5ytxC 3pf5S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 8997.026 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: YBX1, NSEP1, YB1 / Production host: Escherichia coli (E. coli) / References: UniProt: P67809 | ||
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#2: RNA chain | Mass: 2159.299 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.56 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 30 % (v/v) 2-methyl-2,4-pentanediol, 0.1 M sodium acetate, pH 4.5, 25 % (w/v) PEG 1500 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97852 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 12, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97852 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 11696 / % possible obs: 96.4 % / Redundancy: 9.2 % / Net I/σ(I): 26.6 |
Reflection shell | Resolution: 1.6→1.66 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3PF5 Resolution: 1.6→30 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.64
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→30 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -6.2485 Å / Origin y: 23.1717 Å / Origin z: 36.1764 Å
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Refinement TLS group | Selection details: all |