+Open data
-Basic information
Entry | Database: PDB / ID: 7eiu | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Mei2 RRM3 in complex with 8mer meiRNA | ||||||
Components |
| ||||||
Keywords | RNA BINDING PROTEIN / Mei2 / RRM / meiRNA | ||||||
Function / homology | Function and homology information Tor2-Mei2-Ste11 complex / cell cycle switching, mitotic to meiotic cell cycle / negative regulation of conjugation with zygote / positive regulation of metaphase/anaphase transition of meiosis II / Mei2 nuclear dot complex / positive regulation of meiotic cell cycle / poly(U) RNA binding / lncRNA binding / nuclear chromosome / protein sequestering activity ...Tor2-Mei2-Ste11 complex / cell cycle switching, mitotic to meiotic cell cycle / negative regulation of conjugation with zygote / positive regulation of metaphase/anaphase transition of meiosis II / Mei2 nuclear dot complex / positive regulation of meiotic cell cycle / poly(U) RNA binding / lncRNA binding / nuclear chromosome / protein sequestering activity / meiotic cell cycle / RNA binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Schizosaccharomyces pombe (fission yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.349 Å | ||||||
Authors | Shen, S.Y. / Lv, M.Q. | ||||||
Citation | Journal: J Mol Cell Biol / Year: 2022 Title: Structural insights reveal the specific recognition of meiRNA by the Mei2 protein. Authors: Shen, S. / Jian, Y. / Cai, Z. / Li, F. / Lv, M. / Liu, Y. / Wu, J. / Fu, C. / Shi, Y. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7eiu.cif.gz | 149.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7eiu.ent.gz | 114.6 KB | Display | PDB format |
PDBx/mmJSON format | 7eiu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7eiu_validation.pdf.gz | 476.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7eiu_full_validation.pdf.gz | 476.9 KB | Display | |
Data in XML | 7eiu_validation.xml.gz | 14.3 KB | Display | |
Data in CIF | 7eiu_validation.cif.gz | 19.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ei/7eiu ftp://data.pdbj.org/pub/pdb/validation_reports/ei/7eiu | HTTPS FTP |
-Related structure data
Related structure data | 7eioSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 17992.529 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) Strain: 972 / ATCC 24843 / Gene: mei2, SPAC27D7.03c / Production host: Escherichia coli (E. coli) / References: UniProt: P08965 #2: RNA chain | Mass: 1829.109 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Schizosaccharomyces pombe (fission yeast) #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.27 Å3/Da / Density % sol: 62.41 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2M Ammoniun Sulfate, 20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 14, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.349→33.114 Å / Num. obs: 21980 / % possible obs: 99.9 % / Redundancy: 7.3 % / CC1/2: 0.994 / Rmerge(I) obs: 0.119 / Net I/σ(I): 18.15 |
Reflection shell | Resolution: 2.349→2.39 Å / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 2.91 / Num. unique obs: 1059 / CC1/2: 0.803 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7EIO Resolution: 2.349→33.114 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.44 / 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: 98.28 Å2 / Biso mean: 34.8099 Å2 / Biso min: 16.05 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.349→33.114 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|