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Yorodumi- PDB-7f3k: Crystal structure of human YBX2 CSD in complex with m5C RNA in sp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7f3k | ||||||
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Title | Crystal structure of human YBX2 CSD in complex with m5C RNA in space group P21212 | ||||||
Components |
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Keywords | RNA BINDING PROTEIN/RNA / Complex / protein-RNA / YBX / Cold-shock domain / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex | ||||||
Function / homology | Function and homology information translational attenuation / oocyte development / regulation of gene expression / positive regulation of cold-induced thermogenesis / spermatogenesis / nucleic acid binding / transcription by RNA polymerase II / DNA binding / RNA binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å | ||||||
Authors | Zhang, Y. / Huang, Y. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Crystal structure of human YBX2 CSD in complex with m5C RNA in space group P21212 Authors: Zhang, Y. / Huang, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7f3k.cif.gz | 46.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7f3k.ent.gz | 24 KB | Display | PDB format |
PDBx/mmJSON format | 7f3k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f3/7f3k ftp://data.pdbj.org/pub/pdb/validation_reports/f3/7f3k | HTTPS FTP |
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-Related structure data
Related structure data | 6a6jS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 10205.441 Da / Num. of mol.: 1 / Mutation: I92T, Q93K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: YBX2, CSDA3, MSY2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y2T7 | ||||
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#2: RNA chain | Mass: 1827.135 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.76 Å3/Da / Density % sol: 30 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M Tris pH 8.0, 3.2 M Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 24, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→50 Å / Num. obs: 8891 / % possible obs: 99.9 % / Redundancy: 12.5 % / Biso Wilson estimate: 17.23 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 35.3 |
Reflection shell | Resolution: 1.76→1.79 Å / Rmerge(I) obs: 0.104 / Num. unique obs: 409 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6A6J Resolution: 1.76→33.69 Å / SU ML: 0.1477 / Cross valid method: FREE R-VALUE / σ(F): 1.54 / Phase error: 15.8122 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.32 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.76→33.69 Å
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Refine LS restraints |
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LS refinement shell |
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