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Yorodumi- PDB-4v4t: Crystal structure of the whole ribosomal complex with a stop codo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4v4t | |||||||||
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Title | Crystal structure of the whole ribosomal complex with a stop codon in the A-site. | |||||||||
Components |
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Keywords | RIBOSOME / translation | |||||||||
Function / homology | Function and homology information ribosomal large subunit assembly / large ribosomal subunit rRNA binding / large ribosomal subunit / small ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / transferase activity / tRNA binding / rRNA binding / ribosome ...ribosomal large subunit assembly / large ribosomal subunit rRNA binding / large ribosomal subunit / small ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / zinc ion binding / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) Thermus thermophilus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 6.46 Å | |||||||||
Authors | Petry, S. / Brodersen, D.E. / Murphy IV, F.V. / Dunham, C.M. / Selmer, M. / Tarry, M.J. / Kelley, A.C. / Ramakrishnan, V. | |||||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2005 Title: Crystal Structures of the Ribosome in Complex with Release Factors RF1 and RF2 Bound to a Cognate Stop Codon. Authors: Petry, S. / Brodersen, D.E. / Murphy IV, F.V. / Dunham, C.M. / Selmer, M. / Tarry, M.J. / Kelley, A.C. / Ramakrishnan, V. | |||||||||
History |
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Remark 400 | COMPOUND THIS FILE, 2B9O, CONTAINS THE 30S SUBUNIT, TRNAS AND MRNA FROM A CRYSTAL STRUCTURE OF THE ...COMPOUND THIS FILE, 2B9O, CONTAINS THE 30S SUBUNIT, TRNAS AND MRNA FROM A CRYSTAL STRUCTURE OF THE WHOLE RIBOSOMAL COMPLEX WITH A STOP CODON IN THE A-SITE. THE ENTIRE CRYSTAL STRUCTURE CONTAINS ONE 70S RIBOSOME, TRNAS AND MRNA WITH A STOP CODON IN THE A-SITE AND ARE DEPOSITED UNDER 2B9O (30S SUBUNIT AND LIGANDS) AND 2B9P (50S SUBUNIT). |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4v4t.cif.gz | 3.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4v4t.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 4v4t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v4/4v4t ftp://data.pdbj.org/pub/pdb/validation_reports/v4/4v4t | HTTPS FTP |
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-Related structure data
Related structure data | 4v4rC 4v4sC 1j5eS 1nkwS 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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1 |
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Unit cell |
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-Components
-RNA chain , 6 types, 6 molecules AAAVAWAXBBBA
#1: RNA chain | Mass: 493958.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: GenBank: 155076 |
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#2: RNA chain | Mass: 24518.570 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pBs tRNAPhe / Production host: Escherichia coli (E. coli) / Strain (production host): HMS 174 |
#3: RNA chain | Mass: 24743.812 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pBs tRNAPhe / Production host: Escherichia coli (E. coli) / Strain (production host): HMS 174 |
#4: RNA chain | Mass: 5703.420 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: CHEMICALLY SYNTHESIZED AND GEL-PURIFIED SOURCE 24 (DHARMACON) |
#25: RNA chain | Mass: 39846.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: GenBank: 48271 |
#26: RNA chain | Mass: 948280.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: GenBank: 48268 |
-30S ribosomal protein ... , 20 types, 20 molecules ABACADAEAFAGAHAIAJAKALAMANAOAPAQARASATAU
#5: Protein | Mass: 29317.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80371 |
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#6: Protein | Mass: 26751.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80372 |
#7: Protein | Mass: 24373.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80373 |
#8: Protein | Mass: 17583.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P27152, UniProt: Q5SHQ5*PLUS |
#9: Protein | Mass: 11988.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P23370, UniProt: Q5SLP8*PLUS |
#10: Protein | Mass: 18050.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P17291 |
#11: Protein | Mass: 15868.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P24319, UniProt: P0DOY9*PLUS |
#12: Protein | Mass: 14429.661 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P62669, UniProt: P80374*PLUS |
#13: Protein | Mass: 11954.968 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80375, UniProt: Q5SHN7*PLUS |
#14: Protein | Mass: 13737.868 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80376 |
#15: Protein | Mass: 14920.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: GenBank: 55981666, UniProt: Q5SHN3*PLUS |
#16: Protein | Mass: 14338.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80377 |
#17: Protein | Mass: 7158.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P24320, UniProt: P0DOY6*PLUS |
#18: Protein | Mass: 10578.407 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80378, UniProt: Q5SJ76*PLUS |
#19: Protein | Mass: 10409.983 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SJH3 |
#20: Protein | Mass: 12324.670 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P24321, UniProt: P0DOY7*PLUS |
#21: Protein | Mass: 10244.272 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80382, UniProt: Q5SLQ0*PLUS |
#22: Protein | Mass: 10605.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80381, UniProt: Q5SHP2*PLUS |
#23: Protein | Mass: 11722.116 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P62661, UniProt: P80380*PLUS |
#24: Protein/peptide | Mass: 3350.030 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P62612, UniProt: Q5SIH3*PLUS |
+50S ribosomal protein ... , 29 types, 29 molecules BDBEBFBGBHBIBNBOBPBQBSBTBWBXBYBZBRBUBVB2B3B0B4B5B6B7B8B9BK
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 4 |
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-Sample preparation
Crystal | Density Matthews: 4.7 Å3/Da / Density % sol: 73.6 % | ||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 6.7 Details: PEG20k, MES buffer, magnesium acetate, potassium chloride, ammonium chloride, pH 6.7, VAPOR DIFFUSION, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.976269 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 1, 2005 |
Radiation | Monochromator: Khozu monochromator with a McLennon controller containing a LN2 cooled Si111 crystal Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976269 Å / Relative weight: 1 |
Reflection | Resolution: 6.46→100 Å / Num. obs: 123391 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 5 / Redundancy: 11.5 % / Rsym value: 0.131 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 6.46→6.76 Å / Redundancy: 11.1 % / Mean I/σ(I) obs: 2.625 / Num. unique all: 12194 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1J5E, 1NKW Resolution: 6.46→40 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 36535122.44 / Stereochemistry target values: Engh & Huber Details: THIS IS A LOW RESOLUTION STRUCTURE OBTAINED BY USING A MOLECULAR REPLACEMENT MODEL. THE STRUCTURE IS DEPOSITED AS AN ALL-ATOM MODEL ONLY SO THAT OUR REFINEMENT PROCEDURE AND MAPS CAN BE ...Details: THIS IS A LOW RESOLUTION STRUCTURE OBTAINED BY USING A MOLECULAR REPLACEMENT MODEL. THE STRUCTURE IS DEPOSITED AS AN ALL-ATOM MODEL ONLY SO THAT OUR REFINEMENT PROCEDURE AND MAPS CAN BE REPLICATED. THE CONFORMATION OF INDIVIDUAL ATOMS OR SIDE CHAINS, THE REGISTRY OF THE RESIDUES ALONG THE CHAIN, OR EVEN THE DETAILED PATH OF MAIN CHAINS CANNOT BE ASCERTAINED AT THIS RESOLUTION. Chain AX contains only P atoms. There are lots of O3*-P distances that are not within bond distance in both chain AA and chain AW.
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Displacement parameters | Biso mean: 287 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 6.46→40 Å
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LS refinement shell | Highest resolution: 6.46 Å / Rfactor Rfree error: 0.047
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