[English] 日本語
Yorodumi- PDB-5mdu: Structure of the RNA recognition motif (RRM) of Seb1 from S. pombe. -
+Open data
-Basic information
Entry | Database: PDB / ID: 5mdu | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of the RNA recognition motif (RRM) of Seb1 from S. pombe. | ||||||||||||
Components | Rpb7-binding protein seb1 | ||||||||||||
Keywords | TRANSCRIPTION / RNA recognition motif (RRM) / S. pombe / transcription termination / RNA binding | ||||||||||||
Function / homology | Function and homology information Mei2 nuclear dot complex / sno(s)RNA 3'-end processing / co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway / regulatory ncRNA 3'-end processing / mRNA 3'-end processing / lncRNA binding / RNA polymerase II C-terminal domain binding / RNA binding / nucleus Similarity search - Function | ||||||||||||
Biological species | Schizosaccharomyces pombe (fission yeast) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.02 Å | ||||||||||||
Authors | Wittmann, S. / Renner, M. / El Omari, K. / Adams, O. / Vasiljeva, L. / Grimes, J. | ||||||||||||
Funding support | United Kingdom, 3items
| ||||||||||||
Citation | Journal: Nat Commun / Year: 2017 Title: The conserved protein Seb1 drives transcription termination by binding RNA polymerase II and nascent RNA. Authors: Wittmann, S. / Renner, M. / Watts, B.R. / Adams, O. / Huseyin, M. / Baejen, C. / El Omari, K. / Kilchert, C. / Heo, D.H. / Kecman, T. / Cramer, P. / Grimes, J.M. / Vasiljeva, L. | ||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5mdu.cif.gz | 83.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5mdu.ent.gz | 66.1 KB | Display | PDB format |
PDBx/mmJSON format | 5mdu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/md/5mdu ftp://data.pdbj.org/pub/pdb/validation_reports/md/5mdu | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 17377.832 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) Strain: 972 / ATCC 24843 / Gene: seb1, SPAC222.09 / Plasmid: pOPINS3C / Production host: Escherichia coli (E. coli) / Strain (production host): pLysS / References: UniProt: Q9UTE3 | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-CL / | ||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.99 % |
---|---|
Crystal grow | Temperature: 293.65 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 1 M ammonium formate, 100 mM sodium cacodylate, 8% (w/v) poly-gamma-glutamic acid polymer (PGA-LM, 200-400 kDa low molecular weight polymer) |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 10, 2016 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.02→43.34 Å / Num. obs: 79454 / % possible obs: 94.6 % / Redundancy: 6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.045 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 1.02→1.05 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.748 / Mean I/σ(I) obs: 1.3 / CC1/2: 0.545 / % possible all: 57.5 |
-Processing
Software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 1.02→43.34 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 13.06
| ||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.02→43.34 Å
| ||||||||||||||||||||||||
Refine LS restraints |
|