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- PDB-4v4t: Crystal structure of the whole ribosomal complex with a stop codo... -
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Open data
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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. | |||||||||
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![]() | RIBOSOME / translation | |||||||||
Function / homology | ![]() 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 ...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 / tRNA binding / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / zinc ion binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Petry, S. / Brodersen, D.E. / Murphy IV, F.V. / Dunham, C.M. / Selmer, M. / Tarry, M.J. / Kelley, A.C. / Ramakrishnan, V. | |||||||||
![]() | ![]() 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). |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 3.1 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 3.9 MB | Display | |
Data in XML | ![]() | 695.7 KB | Display | |
Data in CIF | ![]() | 927.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4v4rC ![]() 4v4sC ![]() 1j5eS ![]() 1nkwS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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) ![]() ![]() |
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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.) ![]() ![]() ![]() ![]() |
#3: RNA chain | Mass: 24743.812 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#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) ![]() ![]() |
#26: RNA chain | Mass: 948280.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-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) ![]() ![]() |
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#6: Protein | Mass: 26751.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#7: Protein | Mass: 24373.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#8: Protein | Mass: 17583.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#9: Protein | Mass: 11988.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#10: Protein | Mass: 18050.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#11: Protein | Mass: 15868.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#12: Protein | Mass: 14429.661 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#13: Protein | Mass: 11954.968 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#14: Protein | Mass: 13737.868 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#15: Protein | Mass: 14920.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#16: Protein | Mass: 14338.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#17: Protein | Mass: 7158.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#18: Protein | Mass: 10578.407 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#19: Protein | Mass: 10409.983 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#20: Protein | Mass: 12324.670 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#21: Protein | Mass: 10244.272 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#22: Protein | Mass: 10605.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#23: Protein | Mass: 11722.116 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#24: Protein/peptide | Mass: 3350.030 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
+50S ribosomal protein ... , 29 types, 29 molecules BDBEBFBGBHBIBNBOBPBQBSBTBWBXBYBZBRBUBVB2B3B0B4B5B6B7B8B9BK
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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