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- PDB-5ytx: Crystal structure of YB1 cold-shock domain in complex with UCAACU -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ytx | ||||||
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Title | Crystal structure of YB1 cold-shock domain in complex with UCAACU | ||||||
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![]() | RNA BINDING PROTEIN/RNA / YB1 / cold-shock domain / CAAC / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex | ||||||
Function / homology | ![]() tRNA transport / CRD-mediated mRNA stability complex / C5-methylcytidine-containing RNA reader activity / miRNA transport / negative regulation of striated muscle cell differentiation / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Noncanonical activation of NOTCH3 / RNA transport / CRD-mediated mRNA stabilization / protein localization to cytoplasmic stress granule ...tRNA transport / CRD-mediated mRNA stability complex / C5-methylcytidine-containing RNA reader activity / miRNA transport / negative regulation of striated muscle cell differentiation / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Noncanonical activation of NOTCH3 / RNA transport / CRD-mediated mRNA stabilization / protein localization to cytoplasmic stress granule / histone pre-mRNA 3'end processing complex / embryonic morphogenesis / positive regulation of cytoplasmic translation / U12-type spliceosomal complex / 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 / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / P-body / cytoplasmic stress granule / mRNA processing / Interferon gamma signaling / sequence-specific double-stranded DNA binding / GTPase binding / single-stranded DNA binding / regulation of gene expression / double-stranded DNA binding / in utero embryonic development / nucleic acid binding / negative regulation of translation / ribonucleoprotein complex / intracellular membrane-bounded organelle / mRNA binding / 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 | ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yang, X. / Huang, Y. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 52.9 KB | Display | ![]() |
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PDB format | ![]() | 35 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5ytsC ![]() 5yttC ![]() 5ytvC ![]() 3pf5S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() |
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#2: RNA chain | Mass: 1836.149 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.95 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop 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: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 21, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→30 Å / Num. obs: 12349 / % possible obs: 98.9 % / Redundancy: 6 % / Net I/σ(I): 35.4 |
Reflection shell | Resolution: 1.55→1.61 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3PF5 Resolution: 1.551→28.801 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 26.31
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.551→28.801 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: -23.0586 Å / Origin y: -6.8096 Å / Origin z: -35.2714 Å
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Refinement TLS group | Selection details: all |