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Open data
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Basic information
Entry | Database: PDB / ID: 5it8 | |||||||||
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Title | High-resolution structure of the Escherichia coli ribosome | |||||||||
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![]() | RIBOSOME / Protein biosynthesis / ribosomes / RNA / transfer / exit / peptidyl / 30S / 70S / 16S / ribosomal subunit / posttranscriptional modification | |||||||||
Function / homology | ![]() stringent response / mRNA base-pairing translational repressor activity / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity ...stringent response / mRNA base-pairing translational repressor activity / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / translational termination / four-way junction DNA binding / DnaA-L2 complex / translation repressor activity / negative regulation of translational initiation / negative regulation of DNA-templated DNA replication initiation / regulation of mRNA stability / ribosome assembly / mRNA regulatory element binding translation repressor activity / positive regulation of RNA splicing / assembly of large subunit precursor of preribosome / transcription elongation factor complex / DNA endonuclease activity / regulation of DNA-templated transcription elongation / cytosolic ribosome assembly / transcription antitermination / response to reactive oxygen species / regulation of cell growth / DNA-templated transcription termination / maintenance of translational fidelity / response to radiation / ribosomal large subunit assembly / mRNA 5'-UTR binding / large ribosomal subunit / ribosome biogenesis / ribosome binding / 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 / tRNA binding / molecular adaptor activity / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / DNA binding / RNA binding / zinc ion binding / membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Cocozaki, A. / Ferguson, A. | |||||||||
![]() | ![]() Title: Resistance mutations generate divergent antibiotic susceptibility profiles against translation inhibitors. Authors: Cocozaki, A.I. / Altman, R.B. / Huang, J. / Buurman, E.T. / Kazmirski, S.L. / Doig, P. / Prince, D.B. / Blanchard, S.C. / Cate, J.H. / Ferguson, A.D. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 14.3 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 2 MB | Display | |
Data in XML | ![]() | 694.7 KB | Display | |
Data in CIF | ![]() | 1 MB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5j5bC ![]() 5j7lC ![]() 5j88C ![]() 5j8aC ![]() 5j91C ![]() 5jc9C ![]() 4ybbS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
-RNA chain , 4 types, 6 molecules AABACBDBCADA
#1: RNA chain | Mass: 497404.969 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #28: RNA chain | Mass: 38790.090 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #31: RNA chain | | Mass: 941809.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #33: RNA chain | | Mass: 941505.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-30S ribosomal protein ... , 20 types, 40 molecules ABBBACBCADBDAEBEAFBFAGBGAHBHAIBIAJBJAKBKALBLAMBMANBNAOBOAPBP...
#2: Protein | Mass: 24971.764 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #3: Protein | Mass: 23078.785 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #4: Protein | Mass: 23383.002 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #5: Protein | Mass: 16361.878 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #6: Protein | Mass: 12326.251 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #7: Protein | Mass: 16861.523 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #8: Protein | Mass: 14015.361 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #9: Protein | Mass: 14554.882 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #10: Protein | Mass: 11325.117 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #11: Protein | Mass: 12487.200 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #12: Protein | Mass: 13683.053 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #13: Protein | Mass: 12625.753 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #14: Protein | Mass: 11475.364 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #15: Protein | Mass: 10159.621 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #16: Protein | Mass: 9207.572 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #17: Protein | Mass: 9263.946 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #18: Protein | Mass: 6466.477 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #19: Protein | Mass: 9057.626 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #20: Protein | Mass: 9577.268 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #21: Protein | Mass: 6629.744 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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+50S ribosomal protein ... , 31 types, 59 molecules C1D1C2D2C3D3C4D4C5D5C0D0CCDCCDDDCEDECFDFCGDGCHDHCJDJCKDKCLDL...
-Non-polymers , 14 types, 8299 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/PUT.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/SPD.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/ACY.gif)
![](data/chem/img/GUN.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/PUT.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/SPD.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/ACY.gif)
![](data/chem/img/GUN.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/HOH.gif)
#56: Chemical | ChemComp-MG / #57: Chemical | ChemComp-PG4 / #58: Chemical | ChemComp-MPD / ( #59: Chemical | ChemComp-PUT / #60: Chemical | #61: Chemical | ChemComp-PEG / #62: Chemical | ChemComp-EDO / #63: Chemical | ChemComp-PGE / #64: Chemical | ChemComp-SPD / #65: Chemical | #66: Chemical | #67: Chemical | ChemComp-GUN / | #68: Chemical | ChemComp-TRS / | #69: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.39 Å3/Da / Density % sol: 63.68 % |
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Crystal grow | Temperature: 291 K / Method: microbatch / pH: 6.5 / Details: PEG8k, MPD |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 1, 2013 | ||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.117→47.194 Å / % possible obs: 89.4 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 52.53 Å2 / Rmerge(I) obs: 0.122 / Net I/σ(I): 82.3 | ||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4ybb Resolution: 3.12→47.194 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 3.12→47.194 Å
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