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Yorodumi- PDB-4v5k: Structure of cytotoxic domain of colicin E3 bound to the 70S ribosome -
+Open data
-Basic information
Entry | Database: PDB / ID: 4v5k | |||||||||
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Title | Structure of cytotoxic domain of colicin E3 bound to the 70S ribosome | |||||||||
Components |
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Keywords | RIBOSOME | |||||||||
Function / homology | Function and homology information negative regulation of ion transmembrane transporter activity / extrachromosomal circular DNA / endo-alpha-N-acetylgalactosaminidase activity / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / large ribosomal subunit / ribosome binding / Lyases; Phosphorus-oxygen lyases / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly ...negative regulation of ion transmembrane transporter activity / extrachromosomal circular DNA / endo-alpha-N-acetylgalactosaminidase activity / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / large ribosomal subunit / ribosome binding / Lyases; Phosphorus-oxygen lyases / 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 / endonuclease activity / cytosolic large ribosomal subunit / killing of cells of another organism / transmembrane transporter binding / cytoplasmic translation / tRNA binding / rRNA binding / negative regulation of translation / lyase activity / ribosome / structural constituent of ribosome / defense response to bacterium / translation / ribonucleoprotein complex / mRNA binding / zinc ion binding / extracellular region / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli K-12 (bacteria) Escherichia coli (E. coli) Thermus thermophilus HB8 (bacteria) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 3.2 Å | |||||||||
Authors | Ng, C.L. / Lang, K. / Meenan, N.A.G. / Sharma, A. / Kelley, A.C. / Kleanthous, C. / Ramakrishnan, V. | |||||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2010 Title: Structural Basis for 16S Ribosomal RNA Cleavage by the Cytotoxic Domain of Colicin E3. Authors: Ng, C.L. / Lang, K. / Meenan, N.A.G. / Sharma, A. / Kelley, A.C. / Kleanthous, C. / Ramakrishnan, V. #1: Journal: Science / Year: 2006 Title: Structure of the 70S Ribosome Complexed with mRNA and tRNA. Authors: Selmer, M. / Dunham, C.M. / Murphy, F.V. / Weixlbaumer, A. / Petry, S. / Kelley, A.C. / Weir, J.R. / Ramakrishnan, V. | |||||||||
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 | 4v5k.cif.gz | 7.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4v5k.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 4v5k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4v5k_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 4v5k_full_validation.pdf.gz | 4.1 MB | Display | |
Data in XML | 4v5k_validation.xml.gz | 934.9 KB | Display | |
Data in CIF | 4v5k_validation.cif.gz | 1.3 MB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v5/4v5k ftp://data.pdbj.org/pub/pdb/validation_reports/v5/4v5k | HTTPS FTP |
-Related 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 , 6 types, 12 molecules AACAAVAWCVCWAXBADABBDBCX
#1: RNA chain | Mass: 494038.250 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: BOND BETWEEN A1493-G1494 WAS CLEAVED / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: GenBank: 55979969 #22: RNA chain | Mass: 24802.785 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Production host: Escherichia coli #23: RNA chain | | Mass: 8156.980 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #35: RNA chain | Mass: 926365.812 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) #36: RNA chain | Mass: 39494.535 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: GenBank: 55979969 #58: RNA chain | | Mass: 8196.021 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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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: 14429.661 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P62669, 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: 14920.754 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
#24: Protein | Mass: 10874.229 Da / Num. of mol.: 2 / Fragment: RESIDUES 455-551 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli / Production host: Escherichia coli / References: UniProt: P00646 |
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+50S RIBOSOMAL PROTEIN ... , 31 types, 62 molecules B0D0B1D1B2D2B3D3B4D4B5D5B6D6B7D7B8D8B9D9BCDCBDDDBEDEBFDFBGDG...
-Non-polymers , 3 types, 2340 molecules
#59: Chemical | ChemComp-MG / #60: Chemical | ChemComp-ZN / #61: Water | ChemComp-HOH / | |
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-Details
Compound details | ENGINEEREDSequence details | RESIDUE 455-551 (EQUAL TO RESIDUE 0-96 IN CHAIN Y) MUTATION AT RESIDUE H58A (CHAIN Y) | |
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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: 2.96 Å3/Da / Density % sol: 58 % / Description: NONE |
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Crystal grow | pH: 7.18 Details: AS STATED IN STRUCTURE OF THE 70S RIBOSOME COMPLEXED WITH MRNA AND TRNA. (2006) SCIENCE 313: 1935, PH 7.18 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395 |
Detector | Type: ADSC / Detector: CCD / Date: Apr 6, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9395 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→44.53 Å / Num. obs: 960332 / % possible obs: 99.4 % / Observed criterion σ(I): 1.5 / Redundancy: 4.18 % / Biso Wilson estimate: 69.3 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.95 |
-Processing
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 3.2→44.53 Å / Rfactor Rfree error: 0.001 / Data cutoff high absF: 19981437.72 / 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: 50.5777 Å2 / ksol: 0.25 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 113.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.2→44.53 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.2→3.4 Å / Rfactor Rfree error: 0.004 / Total num. of bins used: 6
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Xplor file |
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