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Yorodumi- PDB-6w6c: Structural and catalytic roles of human 18S rRNA methyltransferas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6w6c | ||||||
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Title | Structural and catalytic roles of human 18S rRNA methyltransferases DIMT1 in ribosome assembly and translation | ||||||
Components | Probable dimethyladenosine transferase | ||||||
Keywords | RNA BINDING PROTEIN / RNA modification enzyme | ||||||
Function / homology | Function and homology information 18S rRNA (adenine1779-N6/adenine1780-N6)-dimethyltransferase / 18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase activity / rRNA (adenine-N6,N6-)-dimethyltransferase activity / positive regulation of rRNA processing / rRNA methylation / rRNA modification in the nucleus and cytosol / small-subunit processome / ribosomal small subunit biogenesis / nucleolus / RNA binding ...18S rRNA (adenine1779-N6/adenine1780-N6)-dimethyltransferase / 18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase activity / rRNA (adenine-N6,N6-)-dimethyltransferase activity / positive regulation of rRNA processing / rRNA methylation / rRNA modification in the nucleus and cytosol / small-subunit processome / ribosomal small subunit biogenesis / nucleolus / RNA binding / nucleoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å | ||||||
Authors | Shen, H. / Stoute, J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2020 Title: Structural and catalytic roles of the human 18SrRNA methyltransferases DIMT1 in ribosome assembly and translation. Authors: Shen, H. / Stoute, J. / Liu, K.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6w6c.cif.gz | 286.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6w6c.ent.gz | 192.8 KB | Display | PDB format |
PDBx/mmJSON format | 6w6c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6w6c_validation.pdf.gz | 437 KB | Display | wwPDB validaton report |
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Full document | 6w6c_full_validation.pdf.gz | 442.8 KB | Display | |
Data in XML | 6w6c_validation.xml.gz | 23.4 KB | Display | |
Data in CIF | 6w6c_validation.cif.gz | 33.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w6/6w6c ftp://data.pdbj.org/pub/pdb/validation_reports/w6/6w6c | HTTPS FTP |
-Related structure data
Related structure data | 6w6fC 1zq9S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 35292.434 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DIMT1, DIMT1L, HUSSY-05 / Production host: Escherichia coli (E. coli) References: UniProt: Q9UNQ2, 18S rRNA (adenine1779-N6/adenine1780-N6)-dimethyltransferase #2: 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: 3.06 Å3/Da / Density % sol: 59.85 % |
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Crystal grow | Temperature: 285 K / Method: evaporation Details: 0.2 M Ammonium sulfate, 0.1 M Tris pH 48.5, 20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X17B1 / Wavelength: 0.92 Å |
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Feb 15, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.38→50 Å / Num. obs: 35302 / % possible obs: 99.9 % / Redundancy: 13 % / Biso Wilson estimate: 35.77 Å2 / CC1/2: 0.991 / CC star: 0.998 / Net I/σ(I): 16 |
Reflection shell | Resolution: 2.38→2.42 Å / Num. unique obs: 1716 / CC1/2: 0.838 / CC star: 0.955 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1zq9 Resolution: 2.38→48.18 Å / SU ML: 0.3016 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.4159 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.81 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.38→48.18 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 1.43288178868 Å / Origin y: -3.76225836322 Å / Origin z: 37.2524032905 Å
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Refinement TLS group |
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