+Open data
-Basic information
Entry | Database: PDB / ID: 4v7u | |||||||||
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Title | Crystal structure of the E. coli ribosome bound to erythromycin. | |||||||||
Components |
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Keywords | RIBOSOME / Protein biosynthesis / ribosomes / RNA / tRNA / transfer / erythromycin / ketolide / macrolide / antibiotic / exit / peptidyl / 30S / 70S / 16S / ribosomal subunit / small | |||||||||
Function / homology | Function and homology information stringent response / mRNA base-pairing translational repressor activity / ornithine decarboxylase inhibitor activity / misfolded RNA binding / transcription antitermination factor activity, 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 / misfolded RNA binding / transcription antitermination factor activity, 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 / DnaA-L2 complex / four-way junction DNA binding / 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 / response to reactive oxygen species / assembly of large subunit precursor of preribosome / transcription elongation factor complex / positive regulation of RNA splicing / DNA endonuclease activity / : / cytosolic ribosome assembly / regulation of DNA-templated transcription elongation / transcription antitermination / regulation of cell growth / maintenance of translational fidelity / DNA-templated transcription termination / response to radiation / mRNA 5'-UTR binding / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / ribosome binding / large ribosomal subunit / ribosome biogenesis / regulation of translation / small ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / transferase activity / tRNA binding / negative regulation of translation / rRNA binding / molecular adaptor activity / ribosome / structural constituent of ribosome / translation / response to antibiotic / mRNA binding / negative regulation of DNA-templated transcription / DNA binding / RNA binding / zinc ion binding / membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.1 Å | |||||||||
Authors | Dunkle, J.A. / Xiong, L. / Mankin, A.S. / Cate, J.H.D. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2010 Title: Structures of the Escherichia coli ribosome with antibiotics bound near the peptidyl transferase center explain spectra of drug action. Authors: Dunkle, J.A. / Xiong, L. / Mankin, A.S. / Cate, J.H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4v7u.cif.gz | 8.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4v7u.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 4v7u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v7/4v7u ftp://data.pdbj.org/pub/pdb/validation_reports/v7/4v7u | HTTPS FTP |
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-Related structure data
Related structure data | 4v7sC 4v7tC 4v7vC 3i1m 3i1n 3i1o 3i1p C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
-RNA chain , 3 types, 6 molecules AACABADABBDB
#1: RNA chain | Mass: 496892.375 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: AP009048.1 #22: RNA chain | Mass: 941612.375 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 33357927 #23: RNA chain | Mass: 38177.762 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: GenBank: CP000948.1 |
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-30S ribosomal protein ... , 20 types, 40 molecules ABCBACCCADCDAECEAFCFAGCGAHCHAICIAJCJAKCKALCLAMCMANCNAOCOAPCP...
#2: Protein | Mass: 24253.943 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: 23078.785 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: 23383.002 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: 15804.282 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: 11669.371 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: 16861.523 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: 14015.361 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: 14554.882 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: 11196.988 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: 12487.200 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: 13636.961 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: 12625.753 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: 11475.364 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: 10159.621 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: 9263.946 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: 6466.477 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: 9057.626 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: 9506.190 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: 6067.081 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...
-Non-polymers , 4 types, 2072 molecules
#53: Chemical | ChemComp-MG / #54: Chemical | ChemComp-ERY / | #55: Chemical | #56: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.4 Å3/Da / Density % sol: 63.8 % |
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Crystal grow | Temperature: 291 K / Method: microbatch / pH: 6.5 Details: 4.3% PEG 8000, 4.9% MPD, 3.8 mM MgCl2, 380 mM NH4Cl, 5.5 mM putrescine, 5 mM spermidine, 10 mM Tris, 20 mM MES pH 6.5. 0.25 mM EDTA, microbatch, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1155 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.1155 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.1→82.4 Å / Num. all: 925719 / Num. obs: 925719 / % possible obs: 83.85 % / Observed criterion σ(F): 1.1 / Observed criterion σ(I): 1.1 / Redundancy: 3.3 % / Rmerge(I) obs: 0.101 / Χ2: 0.943 / Net I/σ(I): 10.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 3I1M, 3I1N, 3I1O, 3I1P Resolution: 3.1→82.4 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 3.22 / σ(F): 1.1 / Phase error: 24.73 / Stereochemistry target values: Phenix
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT / Bsol: 36.707 Å2 / ksol: 0.233 e/Å3 | ||||||||||||||||||||||||
Displacement parameters | Biso max: 421.63 Å2 / Biso mean: 95.1409 Å2 / Biso min: 3.29 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→82.4 Å
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Refine LS restraints |
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