+Open data
-Basic information
Entry | Database: PDB / ID: 5o8m | ||||||
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Title | Crystal structure of the MmI1 YTH domain | ||||||
Components | YTH domain-containing protein mmi1 | ||||||
Keywords | RNA BINDING PROTEIN / YTH domain / meiotic regulator | ||||||
Function / homology | Function and homology information : / lncRNA catabolic process / regulation of termination of RNA polymerase II transcription, poly(A)-coupled / nuclear RNA surveillance / siRNA-independent facultative heterochromatin formation / regulation of siRNA-independent facultative heterochromatin formation / nuclear exosome focus / nuclear mRNA surveillance of spliceosomal pre-mRNA splicing / nuclear-transcribed mRNA catabolic process, meiosis-specific transcripts / Mei2 nuclear dot complex ...: / lncRNA catabolic process / regulation of termination of RNA polymerase II transcription, poly(A)-coupled / nuclear RNA surveillance / siRNA-independent facultative heterochromatin formation / regulation of siRNA-independent facultative heterochromatin formation / nuclear exosome focus / nuclear mRNA surveillance of spliceosomal pre-mRNA splicing / nuclear-transcribed mRNA catabolic process, meiosis-specific transcripts / Mei2 nuclear dot complex / heterochromatin island / nuclear mRNA surveillance of mRNA 3'-end processing / CCR4-NOT complex binding / protein-RNA adaptor activity / regulatory ncRNA 3'-end processing / N6-methyladenosine-containing RNA reader activity / pre-mRNA binding / lncRNA binding / mRNA destabilization / pre-mRNA intronic binding / mRNA binding / chromatin / DNA binding / RNA binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Schizosaccharomyces pombe (fission yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.45 Å | ||||||
Authors | Brettschneider, J. / Verdel, A. / Kadlec, J. | ||||||
Citation | Journal: EMBO J. / Year: 2017 Title: Selective termination of lncRNA transcription promotes heterochromatin silencing and cell differentiation. Authors: Touat-Todeschini, L. / Shichino, Y. / Dangin, M. / Thierry-Mieg, N. / Gilquin, B. / Hiriart, E. / Sachidanandam, R. / Lambert, E. / Brettschneider, J. / Reuter, M. / Kadlec, J. / Pillai, R. ...Authors: Touat-Todeschini, L. / Shichino, Y. / Dangin, M. / Thierry-Mieg, N. / Gilquin, B. / Hiriart, E. / Sachidanandam, R. / Lambert, E. / Brettschneider, J. / Reuter, M. / Kadlec, J. / Pillai, R. / Yamashita, A. / Yamamoto, M. / Verdel, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5o8m.cif.gz | 232.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5o8m.ent.gz | 186.5 KB | Display | PDB format |
PDBx/mmJSON format | 5o8m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o8/5o8m ftp://data.pdbj.org/pub/pdb/validation_reports/o8/5o8m | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Beg auth comp-ID: SER / Beg label comp-ID: SER / Refine code: 0
NCS ensembles :
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-Components
#1: Protein | Mass: 16510.824 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast) Gene: mmi1, SPCC736.12c / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: O74958 #2: Chemical | ChemComp-GOL / #3: 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: 2.36 Å3/Da / Density % sol: 48 % / Description: rods |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2 M ammonium sulfate, 0.1 M Tris pH 8.5, 25 % PEG3350. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 19, 2013 |
Radiation | Monochromator: Silicon (1 1 1) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97242 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→90.2 Å / Num. obs: 102990 / % possible obs: 98.1 % / Observed criterion σ(I): 2.63 / Redundancy: 4.7 % / CC1/2: 1 / Rmerge(I) obs: 0.088 / Net I/σ(I): 10.68 |
Reflection shell | Resolution: 1.45→1.51 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.63 / Num. unique obs: 11613 / CC1/2: 0.8 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.45→90.17 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.453 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R: 0.068 / ESU R Free: 0.058 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.086 Å2
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Refinement step | Cycle: 1 / Resolution: 1.45→90.17 Å
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Refine LS restraints |
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