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Open data
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Basic information
Entry | Database: PDB / ID: 4v9c | |||||||||
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Title | Allosteric control of the ribosome by small-molecule antibiotics | |||||||||
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![]() | Ribosome/Antibiotic / Nucleic Acid Conformation / Protein Biosynthesis / antibiotic / neomycin / aminoglycoside / RRF / recycling / Ribosome-Antibiotic complex | |||||||||
Function / homology | ![]() cytoplasmic translational termination / stringent response / mRNA base-pairing translational repressor activity / ribosomal large subunit binding / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation ...cytoplasmic translational termination / stringent response / mRNA base-pairing translational repressor activity / ribosomal large subunit binding / 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 | ![]() ![]() ![]() | |||||||||
![]() | Cate, J.H.D. / Pulk, A. / Blanchard, S.C. / Wang, L. / Feldman, M.B. / Wasserman, M.R. / Altman, R. | |||||||||
![]() | ![]() Title: Allosteric control of the ribosome by small-molecule antibiotics. Authors: Wang, L. / Pulk, A. / Wasserman, M.R. / Feldman, M.B. / Altman, R.B. / Doudna Cate, J.H. / Blanchard, S.C. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 7.4 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 6.6 MB | Display | ![]() |
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Full document | ![]() | 8.9 MB | Display | |
Data in XML | ![]() | 940.6 KB | Display | |
Data in CIF | ![]() | 1.3 MB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar 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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Components
-RNA chain , 5 types, 10 molecules AACAAVCVAXCXBADABBDB
#1: RNA chain | Mass: 499690.031 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #22: RNA chain | Mass: 24485.539 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #23: RNA chain | Mass: 7787.751 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: RNA oligonucleotide #24: RNA chain | Mass: 941612.375 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #25: RNA chain | Mass: 38790.090 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: 26781.670 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #3: Protein | Mass: 26031.316 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #4: Protein | Mass: 23514.199 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #5: Protein | Mass: 17629.398 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #6: Protein | Mass: 15727.512 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #7: Protein | Mass: 20055.156 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #8: Protein | Mass: 14146.557 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #9: Protein | Mass: 14886.270 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #10: Protein | Mass: 11755.597 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #11: Protein | Mass: 13870.975 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #12: Protein | Mass: 13768.157 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #13: Protein | Mass: 13128.467 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #14: Protein | Mass: 11606.560 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #15: Protein | Mass: 10290.816 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: 9724.491 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #18: Protein | Mass: 9005.472 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #19: Protein | Mass: 10455.355 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #20: Protein | Mass: 9708.464 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #21: Protein | Mass: 8524.039 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 BCDCBDDDBEDEBFDFBGDGBHDHBIDIBJDJBKDKBLDLBMDMBNDNBODOBPDPBQDQ...
-Protein , 1 types, 1 molecules CY
#55: Protein | Mass: 20671.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Non-polymers , 4 types, 2237 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/NMY.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NMY.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
#56: Chemical | ChemComp-MG / #57: Chemical | ChemComp-NMY / #58: Chemical | #59: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61.51 % |
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Crystal grow | Temperature: 291 K / pH: 6.5 / Details: PEG800, MPD, pH 6.5, microbatch, temperature 291K |
-Data collection
Diffraction |
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Detector |
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Radiation |
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Radiation wavelength | Wavelength: 1.111 Å / Relative weight: 1 | |||||||||||||||
Reflection | Highest resolution: 3.3 Å / Num. obs: 793808 / % possible obs: 95.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 98.37 Å2 / Rmerge(I) obs: 0.182 / Net I/σ(I): 5.76 | |||||||||||||||
Reflection shell | Resolution: 3.3→3.39 Å / Rmerge(I) obs: 0.868 / Mean I/σ(I) obs: 1.12 / % possible all: 86.1 |
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Processing
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Refinement | Method to determine structure: ![]()
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Displacement parameters | Biso mean: 151.1 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.3→70 Å
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