+Open data
-Basic information
Entry | Database: PDB / ID: 4v8x | |||||||||
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Title | Structure of Thermus thermophilus ribosome | |||||||||
Components |
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Keywords | RIBOSOME / TOXIN-ANTITOXIN / RIBOSOME-DEPENDENT NUCLEASE / MRNA DEGRADATION / TRANSLATION REGULATION | |||||||||
Function / homology | Function and homology information global gene silencing by mRNA cleavage / toxin-antitoxin complex / single-species biofilm formation / RNA catabolic process / regulation of growth / mRNA catabolic process / ribosomal small subunit binding / negative regulation of translational initiation / RNA endonuclease activity / large ribosomal subunit ...global gene silencing by mRNA cleavage / toxin-antitoxin complex / single-species biofilm formation / RNA catabolic process / regulation of growth / mRNA catabolic process / ribosomal small subunit binding / negative regulation of translational initiation / RNA endonuclease activity / large ribosomal subunit / RNA endonuclease activity, producing 3'-phosphomonoesters / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / response to heat / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / endonuclease activity / cytosolic large ribosomal subunit / tRNA binding / cytoplasmic translation / Hydrolases; Acting on ester bonds / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / regulation of DNA-templated transcription / protein homodimerization activity / RNA binding / zinc ion binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ESCHERICHIA COLI (E. coli) THERMUS THERMOPHILUS (bacteria) SYNTHETIC CONSTRUCT (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.35 Å | |||||||||
Authors | Feng, S. / Chen, Y. / Kamada, K. / Wang, H. / Tang, K. / Wang, M. / Gao, Y.G. | |||||||||
Citation | Journal: Nucleic Acids Res. / Year: 2013 Title: Yoeb-Ribosome Structure: A Canonical Rnase that Requires the Ribosome for its Specific Activity. Authors: Feng, S. / Chen, Y. / Kamada, K. / Wang, H. / Tang, K. / Wang, M. / Gao, Y. | |||||||||
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 | 4v8x.cif.gz | 7.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4v8x.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 4v8x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4v8x_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 4v8x_full_validation.pdf.gz | 3.8 MB | Display | |
Data in XML | 4v8x_validation.xml.gz | 901.8 KB | Display | |
Data in CIF | 4v8x_validation.cif.gz | 1.2 MB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v8/4v8x ftp://data.pdbj.org/pub/pdb/validation_reports/v8/4v8x | HTTPS FTP |
-Related structure data
Related structure data | 3kiq 3kir 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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2 |
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Unit cell |
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-Components
-RNA chain , 7 types, 12 molecules AACAAVAWCVCWAXBADABBDBCX
#1: RNA chain | Mass: 488391.188 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: 70S RIBOSOMES PURIFIED FROM T. THERMOPHILUS / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: GenBank: 55771382 #22: RNA chain | | Mass: 24816.811 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 #23: RNA chain | Mass: 24802.785 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 #24: RNA chain | | Mass: 8246.125 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: SYNTHETIC MRNA WITH ANTI-SHINE DALGARNO SEQUENCE, AAA CODON IN E-SITE, AUG CODON IN P-SITE AND UAG CODON IN A-SITE. A-SITE NUCLEOTIDES HAVE A 2'O-METHOXY MODIFICATION Source: (synth.) SYNTHETIC CONSTRUCT (others) #36: RNA chain | Mass: 926365.812 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: GenBank: 55771382 #37: RNA chain | Mass: 38553.000 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 #59: RNA chain | | Mass: 3259.102 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) |
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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 (bacteria) / Strain: HB8 / References: UniProt: P80371 #3: Protein | Mass: 26751.076 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: P80372 #4: Protein | Mass: 24373.447 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: P80373 #5: Protein | Mass: 17583.416 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: P27152, UniProt: Q5SHQ5 #6: Protein | Mass: 11988.753 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: P23370, UniProt: Q5SLP8 #7: Protein | Mass: 18050.973 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: P17291 #8: Protein | Mass: 15868.570 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 References: UniProt: P24319, UniProt: Q5SHQ2, UniProt: P0DOY9*PLUS #9: Protein | Mass: 14410.614 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: P80374 #10: Protein | Mass: 11954.968 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: P80375, UniProt: Q5SHN7 #11: Protein | Mass: 13737.868 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: P80376 #12: Protein | Mass: 14637.384 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: P17293, UniProt: Q5SHN3 #13: Protein | Mass: 14338.861 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: P80377 #14: Protein | Mass: 7158.725 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 References: UniProt: P24320, UniProt: Q5SHQ1, UniProt: P0DOY6*PLUS #15: Protein | Mass: 10578.407 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: P80378, UniProt: Q5SJ76 #16: Protein | Mass: 10409.983 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: Q5SJH3 #17: Protein | Mass: 12325.655 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: Q5SHP7, UniProt: P0DOY7*PLUS #18: Protein | Mass: 10258.299 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: Q5SLQ0 #19: Protein | Mass: 10605.464 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: P80381, UniProt: Q5SHP2 #20: Protein | Mass: 11736.143 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / 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 (bacteria) / Strain: HB8 / References: UniProt: P62612, UniProt: Q5SIH3 |
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-Protein , 1 types, 4 molecules AYAZCYCZ
#25: Protein | Mass: 10233.658 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Gene: B1563, JW1555, RELE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 References: UniProt: C4ZSA5, UniProt: C8UCW6, UniProt: P69348*PLUS |
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+50S RIBOSOMAL PROTEIN ... , 31 types, 62 molecules B0D0B1D1B2D2B3D3B4D4B5D5B6D6B7D7B8D8B9D9BCDCBDDDBEDEBFDFBGDG...
-Non-polymers , 2 types, 711 molecules
#60: Chemical | ChemComp-MG / #61: Chemical | ChemComp-ZN / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 3.3 Å3/Da / Density % sol: 62.72 % / Description: NONE |
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Crystal grow | pH: 7.1 Details: 0.1 M TRIS-HAC PH 7.2, 0.2 M KSCN, 4.1%-4.3% (W/V) PEG 20K AND 4.1%-4.3% (W/V) PEG 550MME |
-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: Aug 19, 2012 / 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: 3.35→50 Å / Num. obs: 842970 / % possible obs: 99.7 % / Observed criterion σ(I): 1.6 / Redundancy: 5.1 % / Biso Wilson estimate: 75.6 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 3.35→3.4 Å / Redundancy: 4.7 % / Rmerge(I) obs: 1.06 / Mean I/σ(I) obs: 1.6 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 3KIQ,3KIR Resolution: 3.35→49.79 Å / Rfactor Rfree error: 0.001 / Data cutoff high absF: 21486010.91 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 58.5056 Å2 / ksol: 0.3 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 117.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.35→49.79 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.35→3.56 Å / Rfactor Rfree error: 0.004 / Total num. of bins used: 6
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Xplor file |
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