+Open data
-Basic information
Entry | Database: PDB / ID: 5hfz | ||||||
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Title | Mmi1 YTH domain | ||||||
Components | YTH domain-containing protein mmi1 | ||||||
Keywords | RNA BINDING PROTEIN / RNA binding / fission yeast | ||||||
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 / Resolution: 1.96 Å | ||||||
Authors | Chatterjee, D. / Goldgur, Y. / Shuman, S. | ||||||
Citation | Journal: Rna / Year: 2016 Title: Transcription of lncRNA prt, clustered prt RNA sites for Mmi1 binding, and RNA polymerase II CTD phospho-sites govern the repression of pho1 gene expression under phosphate-replete conditions in fission yeast. Authors: Chatterjee, D. / Sanchez, A.M. / Goldgur, Y. / Shuman, S. / Schwer, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5hfz.cif.gz | 150.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hfz.ent.gz | 119.3 KB | Display | PDB format |
PDBx/mmJSON format | 5hfz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hf/5hfz ftp://data.pdbj.org/pub/pdb/validation_reports/hf/5hfz | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 19390.027 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) Strain: 972 / ATCC 24843 / Gene: mmi1, SPCC736.12c / Plasmid: pET28b-His10Smt3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / 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: 2.32 Å3/Da / Density % sol: 46.99 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.3 Details: 0.1 M lithium chloride, 0.1 M Hepes (pH 7.3), 25% PEG6000. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 18, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. obs: 46677 / % possible obs: 86.3 % / Redundancy: 3.3 % / Net I/σ(I): 24.8 |
Reflection shell | Resolution: 1.95→2 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.531 / Mean I/σ(I) obs: 2.9 / % possible all: 58 |
-Processing
Software |
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Refinement | Resolution: 1.96→49.761 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.87 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.96→49.761 Å
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Refine LS restraints |
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LS refinement shell |
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