+Open data
-Basic information
Entry | Database: PDB / ID: 5eip | ||||||
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Title | apo-structure of YTH domain of SpMmi1 | ||||||
Components | YTH domain-containing protein mmi1 | ||||||
Keywords | RNA BINDING PROTEIN / YTH / Mmi1 / DSR | ||||||
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 972h- (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.49 Å | ||||||
Authors | Wu, B.X. / Xu, J.H. / Su, S.C. / Ma, J.B. | ||||||
Citation | Journal: Biochem. Biophys. Res. Commun. / Year: 2017 Title: Structural insights into the specific recognition of DSR by the YTH domain containing protein Mmi1 Authors: Wu, B.X. / Xu, J.H. / Su, S.C. / Liu, H. / Gan, J. / Ma, J.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5eip.cif.gz | 69.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5eip.ent.gz | 51.1 KB | Display | PDB format |
PDBx/mmJSON format | 5eip.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ei/5eip ftp://data.pdbj.org/pub/pdb/validation_reports/ei/5eip | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 15210.191 Da / Num. of mol.: 2 / Fragment: UNP residues 349-477 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe 972h- (yeast) Strain: 972h- / Gene: mmi1, SPCC736.12c / Production host: Escherichia coli (E. coli) / References: UniProt: O74958 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.63 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 20% PEG3350, 0.1M Bis-Tris |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å |
Detector | Type: RIGAKU / Detector: CCD / Date: Apr 3, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.49→59.81 Å / Num. obs: 40097 / % possible obs: 98.5 % / Redundancy: 11.8 % / Net I/σ(I): 16.96 |
-Processing
Software |
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Refinement | Resolution: 1.49→59.81 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.934 / SU B: 1.589 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.084 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.951 Å2
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Refinement step | Cycle: 1 / Resolution: 1.49→59.81 Å
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Refine LS restraints |
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