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Yorodumi- PDB-6b4v: Antibiotic blasticidin S and E. coli release factor 1 bound to th... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6b4v | |||||||||
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Title | Antibiotic blasticidin S and E. coli release factor 1 bound to the 70S ribosome | |||||||||
Components |
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Keywords | RIBOSOME/ANTIBIOTIC / termination suppression / class I release factors / RF1 / stop-codon recognition / termination / blasticidin S / RIBOSOME-ANTIBIOTIC complex | |||||||||
Function / homology | Function and homology information translation release factor activity, codon specific / large ribosomal subunit / 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 ...translation release factor activity, codon specific / large ribosomal subunit / 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 / mRNA binding / zinc ion binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Thermus thermophilus HB27 (bacteria) Escherichia coli K-12 (bacteria) Escherichia coli (E. coli) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å | |||||||||
Authors | Svidritskiy, E. / Korostelev, A.A. | |||||||||
Funding support | United States, 2items
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Citation | Journal: J. Mol. Biol. / Year: 2018 Title: Mechanism of Inhibition of Translation Termination by Blasticidin S. Authors: Svidritskiy, E. / Korostelev, A.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6b4v.cif.gz | 9.8 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6b4v.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6b4v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6b4v_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 6b4v_full_validation.pdf.gz | 2.8 MB | Display | |
Data in XML | 6b4v_validation.xml.gz | 470.5 KB | Display | |
Data in CIF | 6b4v_validation.cif.gz | 738.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b4/6b4v ftp://data.pdbj.org/pub/pdb/validation_reports/b4/6b4v | 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 , 5 types, 12 molecules AEBBFBCGBDIAHBMCHALC
#1: RNA chain | Mass: 489561.188 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: GenBank: 46197919 #2: RNA chain | Mass: 936785.625 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: GenBank: 46197919 #3: RNA chain | Mass: 38882.207 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: GenBank: 46197919 #4: RNA chain | Mass: 24846.902 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) #34: RNA chain | Mass: 7545.634 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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+50S ribosomal protein ... , 29 types, 58 molecules EIBFJBGKBHLBIMBJNBKOBLPBMQBNRBOSBPTBQUBRVBSWB...
-Protein , 1 types, 2 molecules JANC
#35: Protein | Mass: 41644.449 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A7ZKY5 |
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-30S ribosomal protein ... , 20 types, 40 molecules KAOCLAPCMAQCNARCOASCPATCQAUCRAVCSAWCTAXCUAYCVAZCWAADXABDYACD...
#36: Protein | Mass: 29317.703 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62662 #37: Protein | Mass: 26751.076 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62663 #38: Protein | Mass: 24373.447 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62664 #39: Protein | Mass: 17583.416 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62665 #40: Protein | Mass: 11988.753 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62666 #41: Protein | Mass: 18050.973 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62667 #42: Protein | Mass: 15868.570 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62668 #43: Protein | Mass: 14429.661 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62669 #44: Protein | Mass: 11954.968 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62653 #45: Protein | Mass: 13737.868 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62654 #46: Protein | Mass: 14683.476 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P61941 #47: Protein | Mass: 14338.861 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62655 #48: Protein | Mass: 7158.725 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62656 #49: Protein | Mass: 10578.407 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62657 #50: Protein | Mass: 10409.983 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62238 #51: Protein | Mass: 12324.670 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62658 #52: Protein | Mass: 10258.299 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62659 #53: Protein | Mass: 10605.464 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62660 #54: Protein | Mass: 11722.116 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62661 #55: Protein/peptide | Mass: 3350.030 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62611, UniProt: P62613*PLUS |
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-Non-polymers , 3 types, 1695 molecules
#56: Chemical | ChemComp-MG / #57: Chemical | #58: Chemical | ChemComp-ZN / |
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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: 3.32 Å3/Da / Density % sol: 62.98 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 3 uL 70S*mRNA*tRNAfMet*RF1*antibiotic complex + 3 uL crystallization buffer (0.1 M Tris-HCl, pH 7.5, 4% v/v PEG20000, 8% v/v MPD, 0.2 M potassium thiocyanate). 4-fold molar excess of E. coli ...Details: 3 uL 70S*mRNA*tRNAfMet*RF1*antibiotic complex + 3 uL crystallization buffer (0.1 M Tris-HCl, pH 7.5, 4% v/v PEG20000, 8% v/v MPD, 0.2 M potassium thiocyanate). 4-fold molar excess of E. coli release factor 1 and 1 mM blasticidin S were added during complex formation. Reservoir: 300 uL 0.4-0.6 M sodium chloride. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 19, 2015 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→70 Å / Num. obs: 813599 / % possible obs: 99.9 % / Redundancy: 6.5 % / Net I/σ(I): 6.89 |
Reflection shell | Highest resolution: 3.4 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.4→50 Å / Cross valid method: FREE R-VALUE /
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