+Open data
-Basic information
Entry | Database: PDB / ID: 4v4r | |||||||||
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Title | Crystal structure of the whole ribosomal complex. | |||||||||
Components |
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Keywords | RIBOSOME / translation / release factor | |||||||||
Function / homology | Function and homology information translation release factor activity, codon specific / endo-alpha-N-acetylgalactosaminidase activity / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / ribosomal large subunit biogenesis / large ribosomal subunit / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity ...translation release factor activity, codon specific / endo-alpha-N-acetylgalactosaminidase activity / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / ribosomal large subunit biogenesis / 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 / 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 | Escherichia coli (E. coli) Thermus thermophilus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 5.9 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, 2B64, CONTAINS THE 30S SUBUNIT, TRNAS, MRNA AND RELEASE FACTOR RF1 FROM A ...COMPOUND THIS FILE, 2B64, CONTAINS THE 30S SUBUNIT, TRNAS, MRNA AND RELEASE FACTOR RF1 FROM A CRYSTAL STRUCTURE OF THE WHOLE RIBOSOMAL COMPLEX". THE ENTIRE CRYSTAL STRUCTURE CONTAINS ONE 70S RIBOSOME, TRNAS, MRNA AND RELEASE FACTOR RF1 AND ARE DEPOSITED UNDER 2B64 AND 2B66. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4v4r.cif.gz | 3.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4v4r.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 4v4r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4v4r_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4v4r_full_validation.pdf.gz | 3.7 MB | Display | |
Data in XML | 4v4r_validation.xml.gz | 681 KB | Display | |
Data in CIF | 4v4r_validation.cif.gz | 907.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v4/4v4r ftp://data.pdbj.org/pub/pdb/validation_reports/v4/4v4r | HTTPS FTP |
-Related structure data
Related structure data | 4v4sC 4v4tC 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 (Dharmacon) |
#26: 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 |
#27: 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 |
-Protein , 1 types, 1 molecules AY
#25: Protein | Mass: 40153.531 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: prfA / Plasmid: pET42bTEV / Production host: Escherichia coli (E. coli) / References: UniProt: P96077 |
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+50S ribosomal protein ... , 29 types, 29 molecules BDBEBFBGBHBIBNBOBPBQBSBTBWBXBYBZBRBUBVB2B3B0B4B5B6B7B8B9BK
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 4.7 Å3/Da / Density % sol: 73.8 % | ||||||||||||||||||||||||||||||||||||||||||||
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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: 0.97889 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 18, 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: 0.97889 Å / Relative weight: 1 |
Reflection | Resolution: 5.9→100 Å / Num. obs: 149562 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 5 / Redundancy: 7.8 % / Rsym value: 0.134 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 5.9→6.2 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 14940 / Rsym value: 0.831 / % possible all: 96.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1J5E, 1NKW Resolution: 5.9→40 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / 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 and chain AY contains only CA atoms. Some residues are not within link distance. Some C-N distances are more than 2 A and O3*-P distances are more than 3A.
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Displacement parameters | Biso mean: 249.6 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 5.9→40 Å
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LS refinement shell | Resolution: 5.9→5.94 Å
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