+Open data
-Basic information
Entry | Database: PDB / ID: 5cyj | ||||||
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Title | X-ray structure of human RBPMS | ||||||
Components | RNA-binding protein with multiple splicing | ||||||
Keywords | RNA BINDING PROTEIN / RRM domain / RNA-binding protein | ||||||
Function / homology | Function and homology information : / poly(A) binding / positive regulation of SMAD protein signal transduction / RNA processing / P-body / cytoplasmic stress granule / response to oxidative stress / transcription coactivator activity / mRNA binding / protein homodimerization activity ...: / poly(A) binding / positive regulation of SMAD protein signal transduction / RNA processing / P-body / cytoplasmic stress granule / response to oxidative stress / transcription coactivator activity / mRNA binding / protein homodimerization activity / RNA binding / nucleoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.79 Å | ||||||
Authors | Teplova, M. / Farazi, T.A. / Patel, D.J. | ||||||
Funding support | United States, 1items
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Citation | Journal: Q. Rev. Biophys. / Year: 2016 Title: Structural basis underlying CAC RNA recognition by the RRM domain of dimeric RNA-binding protein RBPMS. Authors: Teplova, M. / Farazi, T.A. / Tuschl, T. / Patel, D.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5cyj.cif.gz | 47.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5cyj.ent.gz | 37.1 KB | Display | PDB format |
PDBx/mmJSON format | 5cyj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cy/5cyj ftp://data.pdbj.org/pub/pdb/validation_reports/cy/5cyj | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 11184.552 Da / Num. of mol.: 2 / Fragment: RRM domain (UNP residues 14-110) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RBPMS, HERMES / Production host: Escherichia coli (E. coli) / References: UniProt: Q93062 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.38 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 8.5 Details: 0.2 M lithium sulfate, 0.1M Tris-HCl pH 8.5, 40% (v/v) PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 3, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→61.5 Å / Num. obs: 17458 / % possible obs: 99.9 % / Redundancy: 8.5 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 17 |
Reflection shell | Resolution: 1.79→1.89 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 2.2 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.79→61.5 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 25.57 / Stereochemistry target values: ML
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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: 29.68 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.79→61.5 Å
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Refine LS restraints |
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LS refinement shell |
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