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Yorodumi- PDB-5m0h: Crystal structure of the central flexible region of ASH1 mRNA E3-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5m0h | ||||||
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Title | Crystal structure of the central flexible region of ASH1 mRNA E3-localization element | ||||||
Components | ASH1 E3 (42 nt-TL/TLR) | ||||||
Keywords | RNA / She2p / She3p / ASH1-mRNA / mRNA transport | ||||||
Function / homology | RNA / RNA (> 10) Function and homology information | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | ||||||
Authors | Edelmann, F.T. / Janowski, R. / Niessing, D. | ||||||
Citation | Journal: Nat. Struct. Mol. Biol. / Year: 2017 Title: Molecular architecture and dynamics of ASH1 mRNA recognition by its mRNA-transport complex. Authors: Edelmann, F.T. / Schlundt, A. / Heym, R.G. / Jenner, A. / Niedner-Boblenz, A. / Syed, M.I. / Paillart, J.C. / Stehle, R. / Janowski, R. / Sattler, M. / Jansen, R.P. / Niessing, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5m0h.cif.gz | 33.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5m0h.ent.gz | 22.7 KB | Display | PDB format |
PDBx/mmJSON format | 5m0h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5m0h_validation.pdf.gz | 407 KB | Display | wwPDB validaton report |
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Full document | 5m0h_full_validation.pdf.gz | 407.8 KB | Display | |
Data in XML | 5m0h_validation.xml.gz | 3.6 KB | Display | |
Data in CIF | 5m0h_validation.cif.gz | 4.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m0/5m0h ftp://data.pdbj.org/pub/pdb/validation_reports/m0/5m0h | HTTPS FTP |
-Related structure data
Related structure data | 5m0iC 5m0jC 4fnjS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: RNA chain | Mass: 13504.076 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) |
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#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 57.28 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / Details: 50 mM MES, pH 6.0, 5 % (w/v) PEG 4000, 5 mM MgSO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 1, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→50 Å / Num. obs: 4920 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.24 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 19.93 |
Reflection shell | Resolution: 2.65→2.72 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.27 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4FNJ Resolution: 2.65→45.481 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.89
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.65→45.481 Å
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Refine LS restraints |
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LS refinement shell |
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