+Open data
-Basic information
Entry | Database: PDB / ID: 4v9c | |||||||||
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Title | Allosteric control of the ribosome by small-molecule antibiotics | |||||||||
Components |
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Keywords | Ribosome/Antibiotic / Nucleic Acid Conformation / Protein Biosynthesis / antibiotic / neomycin / aminoglycoside / RRF / recycling / Ribosome-Antibiotic complex | |||||||||
Function / homology | Function and homology information cytoplasmic translational termination / stringent response / 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 ...cytoplasmic translational termination / stringent response / 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 / four-way junction DNA binding / translational termination / DnaA-L2 complex / translation repressor activity / negative regulation of translational initiation / negative regulation of DNA-templated DNA replication initiation / regulation of mRNA stability / mRNA regulatory element binding translation repressor activity / ribosome assembly / positive regulation of RNA splicing / assembly of large subunit precursor of preribosome / transcription elongation factor complex / cytosolic ribosome assembly / regulation of DNA-templated transcription elongation / DNA endonuclease activity / ribosomal large subunit assembly / transcription antitermination / response to reactive oxygen species / regulation of cell growth / DNA-templated transcription termination / maintenance of translational fidelity / response to radiation / 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 / cytoplasmic translation / tRNA binding / molecular adaptor activity / 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 | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.3 Å | |||||||||
Authors | Cate, J.H.D. / Pulk, A. / Blanchard, S.C. / Wang, L. / Feldman, M.B. / Wasserman, M.R. / Altman, R. | |||||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2012 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4v9c.cif.gz | 7.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4v9c.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 4v9c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4v9c_validation.pdf.gz | 6.6 MB | Display | wwPDB validaton report |
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Full document | 4v9c_full_validation.pdf.gz | 8.9 MB | Display | |
Data in XML | 4v9c_validation.xml.gz | 940.6 KB | Display | |
Data in CIF | 4v9c_validation.cif.gz | 1.3 MB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v9/4v9c ftp://data.pdbj.org/pub/pdb/validation_reports/v9/4v9c | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-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) Escherichia coli (E. coli) / Strain: K-12 / References: GenBank: AP012306.1 #22: RNA chain | Mass: 24485.539 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: GenBank: AP012306 #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) Escherichia coli (E. coli) / Strain: K-12 / References: GenBank: AP012306 #25: RNA chain | Mass: 38790.090 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: GenBank: AP012306 |
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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) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P0A7V0 #3: Protein | Mass: 26031.316 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P0A7V3 #4: Protein | Mass: 23514.199 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P0A7V8 #5: Protein | Mass: 17629.398 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P0A7W1 #6: Protein | Mass: 15727.512 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P02358 #7: Protein | Mass: 20055.156 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P02359 #8: Protein | Mass: 14146.557 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P0A7W7 #9: Protein | Mass: 14886.270 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P0A7X3 #10: Protein | Mass: 11755.597 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P0A7R5 #11: Protein | Mass: 13870.975 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P0A7R9 #12: Protein | Mass: 13768.157 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P0A7S3 #13: Protein | Mass: 13128.467 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P0A7S9 #14: Protein | Mass: 11606.560 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P0AG59 #15: Protein | Mass: 10290.816 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P0ADZ4 #16: Protein | Mass: 9207.572 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P0A7T3 #17: Protein | Mass: 9724.491 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P0AG63 #18: Protein | Mass: 9005.472 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P0A7T7 #19: Protein | Mass: 10455.355 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P0A7U3 #20: Protein | Mass: 9708.464 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P0A7U7 #21: Protein | Mass: 8524.039 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P68679 |
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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) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P0A805 |
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-Non-polymers , 4 types, 2237 molecules
#56: Chemical | ChemComp-MG / #57: Chemical | ChemComp-NMY / #58: Chemical | #59: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 16 |
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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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Diffraction source |
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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 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 3.3→70 Å / Occupancy max: 1 / Occupancy min: 0.59 / σ(F): 3.3 / Stereochemistry target values: ENGH & HUBER
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Displacement parameters | Biso mean: 151.1 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.3→70 Å
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