+Open data
-Basic information
Entry | Database: PDB / ID: 5det | ||||||
---|---|---|---|---|---|---|---|
Title | X-ray structure of human RBPMS in complex with the RNA | ||||||
Components |
| ||||||
Keywords | RNA BINDING PROTEIN/RNA / RRM domain / RNA binding protein / RNA BINDING PROTEIN-RNA complex | ||||||
Function / homology | Function and homology information : / poly(A) binding / positive regulation of SMAD protein signal transduction / RNA processing / P-body / cytoplasmic stress granule / transcription coactivator activity / response to oxidative stress / mRNA binding / protein homodimerization activity ...: / poly(A) binding / positive regulation of SMAD protein signal transduction / RNA processing / P-body / cytoplasmic stress granule / transcription coactivator activity / response to oxidative stress / mRNA binding / protein homodimerization activity / RNA binding / nucleoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Teplova, M. / Farazi, T.A. / Tuschl, T. / Patel, D.J. | ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5det.cif.gz | 98.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5det.ent.gz | 74 KB | Display | PDB format |
PDBx/mmJSON format | 5det.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5det_validation.pdf.gz | 466.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5det_full_validation.pdf.gz | 469.3 KB | Display | |
Data in XML | 5det_validation.xml.gz | 11.1 KB | Display | |
Data in CIF | 5det_validation.cif.gz | 15.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/de/5det ftp://data.pdbj.org/pub/pdb/validation_reports/de/5det | HTTPS FTP |
-Related structure data
Related structure data | 5cyjSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 11072.723 Da / Num. of mol.: 2 / Fragment: UNP residues 14-111 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: RNA chain | | Mass: 1506.944 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) #3: RNA chain | | Mass: 1200.778 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) #4: Chemical | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 36.96 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M Bis-Tris-HCl pH 6.5, 28% (w/v) PEG 2000 MME |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97919 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 3, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97919 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→90 Å / Num. obs: 17527 / % possible obs: 99.4 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 10 |
Reflection shell | Resolution: 1.79→1.88 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.775 / Mean I/σ(I) obs: 1.8 / Num. unique all: 2559 / % possible all: 99.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5CYJ Resolution: 1.95→19.867 Å / FOM work R set: 0.781 / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 27.87 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 81.93 Å2 / Biso mean: 27.93 Å2 / Biso min: 9.12 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.95→19.867 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|