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Yorodumi- PDB-3oij: Crystal structure of Saccharomyces Cerevisiae Nep1/Emg1 bound to ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3oij | ||||||
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Title | Crystal structure of Saccharomyces Cerevisiae Nep1/Emg1 bound to S-adenosylhomocysteine and 2 molecules of cognate RNA | ||||||
Components |
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Keywords | RIBOSOMAL PROTEIN / EMG1 / scNEP1 / SPOUT / ribosome biogenesis / methyltransferase / rRNA processing | ||||||
Function / homology | Function and homology information rRNA small subunit pseudouridine methyltransferase Nep1 / nuclear microtubule / rRNA (pseudouridine) methyltransferase activity / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA base methylation / rRNA methylation / Major pathway of rRNA processing in the nucleolus and cytosol / 90S preribosome / 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) ...rRNA small subunit pseudouridine methyltransferase Nep1 / nuclear microtubule / rRNA (pseudouridine) methyltransferase activity / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA base methylation / rRNA methylation / Major pathway of rRNA processing in the nucleolus and cytosol / 90S preribosome / 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) / nuclear periphery / maturation of SSU-rRNA / small-subunit processome / rRNA processing / ribosomal small subunit biogenesis / rRNA binding / nucleolus / nucleoplasm / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Thomas, S.R. / LaRonde-LeBlanc, N. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2011 Title: Structural insight into the functional mechanism of Nep1/Emg1 N1-specific pseudouridine methyltransferase in ribosome biogenesis. Authors: Thomas, S.R. / Keller, C.A. / Szyk, A. / Cannon, J.R. / Laronde-Leblanc, N.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3oij.cif.gz | 220 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3oij.ent.gz | 173.5 KB | Display | PDB format |
PDBx/mmJSON format | 3oij.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3oij_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 3oij_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 3oij_validation.xml.gz | 21 KB | Display | |
Data in CIF | 3oij_validation.cif.gz | 28.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oi/3oij ftp://data.pdbj.org/pub/pdb/validation_reports/oi/3oij | HTTPS FTP |
-Related structure data
Related structure data | 3o7bC 3oiiC 3oinC 2v3jS C: citing same article (ref.) S: Starting model for refinement |
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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: Protein | Mass: 27993.512 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: EMG1, NEP1, YLR186W, L9470.5 / Plasmid: pdest527 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q06287 #2: RNA chain | Mass: 4437.699 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: Cognate RNA fragment synthesized to mimic natural RNA substrate #3: Chemical | #4: Chemical | ChemComp-MG / | #5: 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: 2.86 Å3/Da / Density % sol: 57.01 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.05M MES, 15mM MgS04, 7% PEG 4000, 20% glycerol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.00931 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 7, 2007 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Kohzu HLD8-24 / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.00931 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.9→30 Å / Num. all: 17064 / Num. obs: 16553 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Χ2: 0.824 / Net I/σ(I): 21.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2V3J Resolution: 3→29.886 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.7812 / SU ML: 0.35 / σ(F): 1.36 / 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 / Bsol: 21.289 Å2 / ksol: 0.274 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 169.32 Å2 / Biso mean: 70.9897 Å2 / Biso min: 20.38 Å2
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Refinement step | Cycle: LAST / Resolution: 3→29.886 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: 5
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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