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Yorodumi- PDB-4v5d: Structure of the Thermus thermophilus 70S ribosome in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4v5d | |||||||||
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Title | Structure of the Thermus thermophilus 70S ribosome in complex with mRNA, paromomycin, acylated A- and P-site tRNAs, and E-site tRNA. | |||||||||
Components |
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Keywords | RIBOSOME / METAL-BINDING / RIBOSOMAL PROTEIN / RIBONUCLEOPROTEIN / TRANSLATION / TRNA-BINDING / RRNA-BINDING / TRNA / MRNA / RNA-BINDING / ZINC-FINGER | |||||||||
Function / homology | Function and homology information endo-alpha-N-acetylgalactosaminidase activity / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / 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 ...endo-alpha-N-acetylgalactosaminidase activity / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / 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 / cytoplasmic translation / tRNA binding / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / zinc ion binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | THERMUS THERMOPHILUS (bacteria) ESCHERICHIA COLI (E. coli) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å | |||||||||
Authors | Voorhees, R.M. / Weixlbaumer, A. / Loakes, D. / Kelley, A.C. / Ramakrishnan, V. | |||||||||
Citation | Journal: Nat. Struct. Mol. Biol. / Year: 2009 Title: Insights into substrate stabilization from snapshots of the peptidyl transferase center of the intact 70S ribosome. Authors: Voorhees, R.M. / Weixlbaumer, A. / Loakes, D. / Kelley, A.C. / 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. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4v5d.cif.gz | 7 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4v5d.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 4v5d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4v5d_validation.pdf.gz | 2.4 MB | Display | wwPDB validaton report |
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Full document | 4v5d_full_validation.pdf.gz | 4.2 MB | Display | |
Data in XML | 4v5d_validation.xml.gz | 892 KB | Display | |
Data in CIF | 4v5d_validation.cif.gz | 1.2 MB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v5/4v5d ftp://data.pdbj.org/pub/pdb/validation_reports/v5/4v5d | HTTPS FTP |
-Related structure data
Related structure data | 4v5cC 2j00 2jl5 2jl7 C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
-RNA chain , 6 types, 14 molecules AACAAVAYCVCYAWCWAXCXBADABBDB
#1: RNA chain | Mass: 493958.281 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: CHAIN A (16S RNA) HAS E.COLI NUMBERING, BASED ON A STRUCTURAL ALIGNMENT WITH THE CORRESPONDING E.COLI STRUCTURE IN 2AVY. Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 #22: RNA chain | Mass: 24615.730 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: UNMODIFIED BASES / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: K12 #23: RNA chain | Mass: 24485.539 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: UNMODIFIED BASES / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: K12 #24: RNA chain | Mass: 3436.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #35: RNA chain | Mass: 917797.000 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: CHAIN A (23S RNA) HAS E.COLI RESIDUE NUMBERING, BASED ON A STRUCTURAL ALIGNMENT WITH THE CORRESPONDING E. COLI STRUCTURE IN 2AW4 Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 #36: RNA chain | Mass: 39494.535 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 |
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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: 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: 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: 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 (bacteria) / Strain: HB8 / References: UniProt: P62669 #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: 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: 14920.754 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-132 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: 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: 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 (bacteria) / Strain: HB8 / References: 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: A0A0N0BLS5*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: 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: Q5SIH3 |
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+50S RIBOSOMAL PROTEIN ... , 30 types, 60 molecules B0D0B1D1B2D2B3D3B4D4B5D5B6D6B7D7B8D8B9D9BCDCBDDDBEDEBFDFBGDG...
-Non-polymers , 3 types, 1354 molecules
#57: Chemical | ChemComp-MG / #58: Chemical | #59: Chemical | ChemComp-ZN / |
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-Details
Nonpolymer details | PAROMOMYCIN (PAR): THIS IS AN ANTIBIOTIC WHICH HAS BEEN USED IN PREVIOUS STRUCTURES FROM OUR LAB I. ...PAROMOMYCI |
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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: 3.33 Å3/Da / Density % sol: 63.09 % / Description: NONE |
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Crystal grow | pH: 7.1 / Details: pH 7.1 |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 20, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→50 Å / Num. obs: 789136 / % possible obs: 97.1 % / Observed criterion σ(I): 1 / Redundancy: 5.6 % / Biso Wilson estimate: 52 Å2 / Rmerge(I) obs: 0.2 / Net I/σ(I): 7.42 |
Reflection shell | Resolution: 3.4→3.5 Å / Redundancy: 2.48 % / Rmerge(I) obs: 0.97 / Mean I/σ(I) obs: 1.04 / % possible all: 75 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2J00 2j00 Resolution: 3.5→50 Å / Rfactor Rfree error: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0 Details: REGIONS OF THE 23S RNA AND SEVERAL 50S SUBUNIT PROTEINS WERE CORRECTED IN THIS STRUCTURE BY RE-EVALUATING DATA FROM 2J01 AND 2JL6 (THE SARCIN-RICIN LOOP, A-SITE FINGER, L1 ARM, AND PROTEINS ...Details: REGIONS OF THE 23S RNA AND SEVERAL 50S SUBUNIT PROTEINS WERE CORRECTED IN THIS STRUCTURE BY RE-EVALUATING DATA FROM 2J01 AND 2JL6 (THE SARCIN-RICIN LOOP, A-SITE FINGER, L1 ARM, AND PROTEINS L28 AND L36) AND BY COMPARISON WITH 3D5B (L2, L9, L13, L15, L21, L23, L31, L35).
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 47.77 Å2 / ksol: 0.3 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 105.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.5→50 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.5→3.72 Å / Rfactor Rfree error: 0.005 / Total num. of bins used: 6
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Xplor file |
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