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Yorodumi- PDB-4v8u: Crystal Structure of 70S Ribosome with Both Cognate tRNAs in the ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4v8u | |||||||||
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Title | Crystal Structure of 70S Ribosome with Both Cognate tRNAs in the E and P Sites Representing an Authentic Elongation Complex. | |||||||||
Components |
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Keywords | RIBOSOME / PROTEIN TRANSLATION | |||||||||
Function / homology | Function and homology information ribosome disassembly / translation elongation factor activity / large ribosomal subunit / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding ...ribosome disassembly / translation elongation factor activity / large ribosomal subunit / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / tRNA binding / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / GTPase activity / mRNA binding / GTP binding / zinc ion binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | THERMUS THERMOPHILUS HB8 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 Å | |||||||||
Authors | Gao, Y.G. / Feng, S. / Chen, Y. | |||||||||
Citation | Journal: PLoS ONE / Year: 2013 Title: Crystal structure of 70S ribosome with both cognate tRNAs in the E and P sites representing an authentic elongation complex. Authors: Feng, S. / Chen, Y. / Gao, Y.G. | |||||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "QA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "QA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4v8u.cif.gz | 7.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4v8u.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 4v8u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4v8u_validation.pdf.gz | 2.7 MB | Display | wwPDB validaton report |
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Full document | 4v8u_full_validation.pdf.gz | 4.7 MB | Display | |
Data in XML | 4v8u_validation.xml.gz | 935.6 KB | Display | |
Data in CIF | 4v8u_validation.cif.gz | 1.3 MB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v8/4v8u ftp://data.pdbj.org/pub/pdb/validation_reports/v8/4v8u | HTTPS FTP |
-Related structure data
Similar structure data |
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-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
-RNA chain , 6 types, 12 molecules AACAAVCVAWCWAXCXBADABBDB
#1: RNA chain | Mass: 493958.281 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / References: GenBank: 55771382 #22: RNA chain | Mass: 24485.539 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) #23: RNA chain | Mass: 24816.811 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) #24: RNA chain | Mass: 8156.980 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) #36: RNA chain | Mass: 947935.438 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / References: GenBank: 55979969 #37: RNA chain | Mass: 39540.617 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / References: GenBank: 55979969 |
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-30S RIBOSOMAL PROTEIN ... , 20 types, 40 molecules ABCBACCCADCDAECEAFCFAGCGAHCHAICIAJCJAKCKALCLAMCMANCNAOCOAPCP...
#2: Protein | Mass: 29317.703 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / References: UniProt: P80371 #3: Protein | Mass: 26751.076 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / References: UniProt: P80372 #4: Protein | Mass: 24373.447 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / References: UniProt: P80373 #5: Protein | Mass: 17583.416 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / References: UniProt: Q5SHQ5 #6: Protein | Mass: 11988.753 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / References: UniProt: Q5SLP8 #7: Protein | Mass: 18050.973 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / References: UniProt: P17291 #8: Protein | Mass: 15868.570 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / References: UniProt: Q5SHQ2, UniProt: A0A0M9AFS9*PLUS #9: Protein | Mass: 14410.614 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / References: UniProt: P80374 #10: Protein | Mass: 11954.968 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / References: UniProt: Q5SHN7 #11: Protein | Mass: 13737.868 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / References: UniProt: P80376 #12: Protein | Mass: 14637.384 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / References: UniProt: Q5SHN3 #13: Protein | Mass: 14338.861 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / References: UniProt: P80377 #14: Protein | Mass: 7158.725 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / References: UniProt: Q5SHQ1, UniProt: A0A0N0BLP2*PLUS #15: Protein | Mass: 10578.407 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / References: UniProt: Q5SJ76 #16: Protein | Mass: 10409.983 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / References: UniProt: Q5SJH3 #17: Protein | Mass: 12325.655 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / References: UniProt: Q5SHP7, UniProt: A0A0N0BLS5*PLUS #18: Protein | Mass: 10258.299 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / References: UniProt: Q5SLQ0 #19: Protein | Mass: 10605.464 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / References: UniProt: Q5SHP2 #20: Protein | Mass: 11736.143 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / References: UniProt: P80380 #21: Protein/peptide | Mass: 3350.030 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / References: UniProt: Q5SIH3 |
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-Protein , 1 types, 2 molecules AYCY
#25: Protein | Mass: 76977.102 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / References: UniProt: Q5SHN5 |
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+50S RIBOSOMAL PROTEIN ... , 30 types, 60 molecules B0D0B1D1B2D2B3D3B4D4B5D5B6D6B7D7B8D8B9D9BCDCBDDDBEDEBFDFBGDG...
-Non-polymers , 4 types, 14 molecules
#58: Chemical | ChemComp-ZN / #59: Chemical | #60: Chemical | #61: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 3.4 Å3/Da / Density % sol: 64 % / Description: NONE |
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Crystal grow | pH: 6.4 Details: 0.1M MES, PH6.5, 8.5-9.0% PEG20K, 0-25MM KCL, pH 6.4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 18, 2011 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.7→50 Å / Num. obs: 657561 / % possible obs: 99.8 % / Observed criterion σ(I): 1.64 / Redundancy: 7.3 % / Biso Wilson estimate: 52.2 Å2 / Rmerge(I) obs: 0.2 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 3.7→3.8 Å / Redundancy: 6.1 % / Rmerge(I) obs: 1.08 / Mean I/σ(I) obs: 1.64 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.7→49.75 Å / Rfactor Rfree error: 0.001 / Data cutoff high absF: 15310062.13 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ML / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 48.7341 Å2 / ksol: 0.3 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 102.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.7→49.75 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTRAINED | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.7→3.93 Å / Rfactor Rfree error: 0.004 / Total num. of bins used: 6
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Xplor file |
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