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- PDB-4w2g: Crystal structure of the Thermus thermophilus 70S ribosome in com... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4w2g | ||||||||||||
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Title | Crystal structure of the Thermus thermophilus 70S ribosome in complex with pactamycin (soaked), mRNA and three deacylated tRNAs in the A, P and E sites | ||||||||||||
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![]() | RIBOSOME/ANTIBIOTIC / Pactamycin / antibiotic / 70S ribosome / inhibition of translation / initiation inhibitor / 30S subunit with pactamycin (soaked) / mRNA / deacylated A- / P- / and E-site tRNAs of the 1st 70S ribosome in the ASU / Functional complex of bacterial 70S ribosome with antibiotic pactamycin (compact conformation) / 50S subunit of the 1st 70S ribosome in the ASU / RIBOSOME-ANTIBIOTIC complex | ||||||||||||
Function / homology | ![]() 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 ...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 / ribonucleoprotein complex / translation / mRNA binding / zinc ion binding / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() ![]() synthetic construct (others) | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Polikanov, Y.S. / Osterman, I.A. / Szal, T. / Tashlitsky, V.N. / Serebryakova, M.V. / Kusochek, P. / Bulkley, D. / Malanicheva, I.A. / Efimenko, T.A. / Efremenkova, O.V. ...Polikanov, Y.S. / Osterman, I.A. / Szal, T. / Tashlitsky, V.N. / Serebryakova, M.V. / Kusochek, P. / Bulkley, D. / Malanicheva, I.A. / Efimenko, T.A. / Efremenkova, O.V. / Konevega, A.L. / Shaw, K.J. / Bogdanov, A.A. / Rodnina, M.V. / Dontsova, O.A. / Mankin, A.S. / Steitz, T.A. / Sergiev, P.V. | ||||||||||||
![]() | ![]() Title: Amicoumacin a inhibits translation by stabilizing mRNA interaction with the ribosome. Authors: Polikanov, Y.S. / Osterman, I.A. / Szal, T. / Tashlitsky, V.N. / Serebryakova, M.V. / Kusochek, P. / Bulkley, D. / Malanicheva, I.A. / Efimenko, T.A. / Efremenkova, O.V. / Konevega, A.L. / ...Authors: Polikanov, Y.S. / Osterman, I.A. / Szal, T. / Tashlitsky, V.N. / Serebryakova, M.V. / Kusochek, P. / Bulkley, D. / Malanicheva, I.A. / Efimenko, T.A. / Efremenkova, O.V. / Konevega, A.L. / Shaw, K.J. / Bogdanov, A.A. / Rodnina, M.V. / Dontsova, O.A. / Mankin, A.S. / Steitz, T.A. / Sergiev, P.V. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 7.6 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Details | This PDB entry contains coordinates for the 30S subunit with pactamycin (soaked), mRNA, deacylated A-, P-, and E-site tRNAs of the 1st 70S ribosome in the ASU. The full biological assembly can be obtained by combining coordinates from this entry and the entry for the 50S subunit of the 1st 70S ribosome. The entire ASU contains two 70S ribosomes. |
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Components
-RNA chain , 6 types, 14 molecules AACAAVCVAWAYCWCYAXCXBADABBDB
#1: RNA chain | Mass: 493652.156 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #22: RNA chain | Mass: 7804.735 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: IDT-Synthesized 24-nt M-F-Stop mRNA / Source: (synth.) synthetic construct (others) #23: RNA chain | Mass: 24645.881 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: Phenylalanine tRNA / Source: (gene. exp.) ![]() ![]() ![]() ![]() #24: RNA chain | Mass: 24846.902 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Initiator Methionine tRNA / Source: (gene. exp.) ![]() ![]() ![]() ![]() #25: RNA chain | Mass: 947895.375 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #26: RNA chain | Mass: 39188.371 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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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) ![]() ![]() #3: Protein | Mass: 26751.076 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #4: Protein | Mass: 24373.447 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #5: Protein | Mass: 17583.416 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #6: Protein | Mass: 11988.753 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #7: Protein | Mass: 18050.973 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #8: Protein | Mass: 15868.570 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #9: Protein | Mass: 14410.614 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #10: Protein | Mass: 11954.968 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #11: Protein | Mass: 13737.868 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #12: Protein | Mass: 14637.384 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #13: Protein | Mass: 14338.861 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #14: Protein | Mass: 7158.725 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #15: Protein | Mass: 10578.407 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #16: Protein | Mass: 10409.983 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #17: Protein | Mass: 12325.655 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #18: Protein | Mass: 10258.299 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #19: Protein | Mass: 10605.464 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #20: Protein | Mass: 11736.143 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #21: Protein/peptide | Mass: 3350.030 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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+50S Ribosomal Protein ... , 29 types, 58 molecules BDDDBEDEBFDFBGDGBHDHBIDIBNDNBODOBPDPBQDQBRDRBSDSBTDTBUDUBVDV...
-Non-polymers , 6 types, 5222 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/PCY.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/K.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PCY.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/K.gif)
![](data/chem/img/HOH.gif)
#56: Chemical | ChemComp-MG / #57: Chemical | #58: Chemical | #59: Chemical | ChemComp-ZN / #60: Chemical | #61: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 62.46 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion / pH: 7.6 Details: 0.1-0.2 M Arginine-HCl, 0.1M Tris-HCl pH 7.6, 2.5% PEG-20K, 7-12% MPD, 0.5 mM BME, VAPOR DIFFUSION, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 9, 2013 / Details: S/N 60-0112-F | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.55→310.99 Å / Num. all: 1876459 / Num. obs: 1857656 / % possible obs: 99 % / Observed criterion σ(F): 1 / Observed criterion σ(I): -3 / Redundancy: 3.723 % / Biso Wilson estimate: 48.21 Å2 / Rmerge(I) obs: 0.139 / Χ2: 1.068 / Net I/σ(I): 7.61 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Rmerge(I) obs: 0.012 / Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 139.79 Å2 / Biso mean: 58.21 Å2 / Biso min: 22.05 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.55→145.516 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30
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