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Yorodumi- PDB-4qtu: Structure of S. cerevisiae Bud23-Trm112 complex involved in forma... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4qtu | ||||||
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Title | Structure of S. cerevisiae Bud23-Trm112 complex involved in formation of m7G1575 on 18S rRNA (SAM bound form) | ||||||
Components |
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Keywords | TRANSFERASE / Class I / Methyltransferase | ||||||
Function / homology | Function and homology information tRNA (m2G10) methyltransferase complex / Methylation / positive regulation of termination of DNA-templated transcription / 18S rRNA (guanine1575-N7)-methyltransferase / eRF1 methyltransferase complex / Eukaryotic Translation Termination / rRNA (guanine-N7)-methylation / tRNA methyltransferase complex / rRNA (guanine) methyltransferase activity / tRNA wobble uridine modification ...tRNA (m2G10) methyltransferase complex / Methylation / positive regulation of termination of DNA-templated transcription / 18S rRNA (guanine1575-N7)-methyltransferase / eRF1 methyltransferase complex / Eukaryotic Translation Termination / rRNA (guanine-N7)-methylation / tRNA methyltransferase complex / rRNA (guanine) methyltransferase activity / tRNA wobble uridine modification / tRNA methylation / ribosomal small subunit export from nucleus / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / maturation of SSU-rRNA / ribosomal small subunit biogenesis / ribosome / protein heterodimerization activity / nucleolus / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae S288c (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.124 Å | ||||||
Authors | Letoquart, J. / Huvelle, E. / Wacheul, L. / Bourgeois, G. / Zorbas, C. / Graille, M. / Heurgue-Hamard, V. / Lafontaine, D.L.J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2014 Title: Structural and functional studies of Bud23-Trm112 reveal 18S rRNA N7-G1575 methylation occurs on late 40S precursor ribosomes. Authors: Letoquart, J. / Huvelle, E. / Wacheul, L. / Bourgeois, G. / Zorbas, C. / Graille, M. / Heurgue-Hamard, V. / Lafontaine, D.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qtu.cif.gz | 145.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qtu.ent.gz | 112 KB | Display | PDB format |
PDBx/mmJSON format | 4qtu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4qtu_validation.pdf.gz | 909.2 KB | Display | wwPDB validaton report |
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Full document | 4qtu_full_validation.pdf.gz | 930.1 KB | Display | |
Data in XML | 4qtu_validation.xml.gz | 26.9 KB | Display | |
Data in CIF | 4qtu_validation.cif.gz | 37.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qt/4qtu ftp://data.pdbj.org/pub/pdb/validation_reports/qt/4qtu | HTTPS FTP |
-Related structure data
Related structure data | 4qttSC 4qtm 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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2 |
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Unit cell |
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-Components
-Protein , 2 types, 4 molecules ACBD
#1: Protein | Mass: 15078.209 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Gene: N3445, TRM112, YNR046W / Production host: Escherichia coli (E. coli) / References: UniProt: P53738 #2: Protein | Mass: 23048.053 Da / Num. of mol.: 2 / Fragment: fragment residues 1-202 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Gene: BUD23, YCR047C, YCR47C / Production host: Escherichia coli (E. coli) References: UniProt: P25627, Transferases; Transferring one-carbon groups; Methyltransferases |
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-Non-polymers , 4 types, 196 molecules
#3: Chemical | #4: Chemical | ChemComp-EDO / #5: Chemical | #6: 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: 2.26 Å3/Da / Density % sol: 45.54 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2012 |
Radiation | Monochromator: Channel cut cryogenically cooled monochromator crystal Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 |
Reflection | Resolution: 2.124→50 Å / Num. obs: 38373 / % possible obs: 94.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 37.1 Å2 |
Reflection shell | Resolution: 2.2→2.33 Å / % possible all: 94.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4QTT Resolution: 2.124→38.307 Å / FOM work R set: 0.8226 / SU ML: 0.27 / σ(F): 1.99 / Phase error: 24.88 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 101.94 Å2 / Biso mean: 44.88 Å2 / Biso min: 19.75 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.124→38.307 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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