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Yorodumi- PDB-4zox: Crystal structure of the Saccharomyces cerevisiae Sqt1 bound to t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4zox | ||||||
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Title | Crystal structure of the Saccharomyces cerevisiae Sqt1 bound to the N-terminus of the ribosomal protein L10 | ||||||
Components |
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Keywords | CHAPERONE / ribosomal biogenesis / WD40 - repeat | ||||||
Function / homology | Function and homology information SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / L13a-mediated translational silencing of Ceruloplasmin expression / translational termination / ribosomal large subunit biogenesis / ribosomal large subunit assembly / unfolded protein binding ...SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / L13a-mediated translational silencing of Ceruloplasmin expression / translational termination / ribosomal large subunit biogenesis / ribosomal large subunit assembly / unfolded protein binding / cytoplasmic translation / cytosolic large ribosomal subunit / structural constituent of ribosome / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Pausch, P. / Altegoer, F. / Bange, G. | ||||||
Citation | Journal: Nat Commun / Year: 2015 Title: Co-translational capturing of nascent ribosomal proteins by their dedicated chaperones. Authors: Pausch, P. / Singh, U. / Ahmed, Y.L. / Pillet, B. / Murat, G. / Altegoer, F. / Stier, G. / Thoms, M. / Hurt, E. / Sinning, I. / Bange, G. / Kressler, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zox.cif.gz | 103.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zox.ent.gz | 75.6 KB | Display | PDB format |
PDBx/mmJSON format | 4zox.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zo/4zox ftp://data.pdbj.org/pub/pdb/validation_reports/zo/4zox | HTTPS FTP |
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-Related structure data
Related structure data | 4zn4C 4zovSC 4zoyC 4zozC 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 41408.727 Da / Num. of mol.: 1 / Fragment: UNP residues 53-431 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: SQT1, YIR012W, YIB12W / Plasmid: pETDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P35184 |
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#2: Protein/peptide | Mass: 3494.010 Da / Num. of mol.: 1 / Fragment: UNP residues 1-20 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: RPL10, GRC5, QSR1, YLR075W / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / References: UniProt: P41805 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 36.76 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.2 M Ca-acetate, 0.1 M Nacacodylate pH 6.5, 40% (v/v) PEG600 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97239 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 13, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97239 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→44.63 Å / Num. obs: 44971 / % possible obs: 99.4 % / Redundancy: 4 % / Net I/σ(I): 18.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ZOV Resolution: 1.6→44.626 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 16.62 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→44.626 Å
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Refine LS restraints |
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LS refinement shell |
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