+Open data
-Basic information
Entry | Database: PDB / ID: 4v9o | |||||||||
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Title | Control of ribosomal subunit rotation by elongation factor G | |||||||||
Components |
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Keywords | Ribosome/antibiotic / Protein biosynthesis / ribosome / RNA / EF-G / elongation / factor / GTP / GDPCP / viomycin / tRNA / tranlocation / exit / peptidyl / 50S / 70S / 23S / ribosomal subunit / Elongation factor G / Ribosome-antibiotic complex | |||||||||
Function / homology | Function and homology information ribosome disassembly / guanosine tetraphosphate binding / translational elongation / 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 ...ribosome disassembly / guanosine tetraphosphate binding / translational elongation / 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 / translation elongation factor activity / translational termination / DnaA-L2 complex / : / four-way junction DNA binding / negative regulation of translational initiation / translation repressor activity / 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 / positive regulation of RNA splicing / DNA endonuclease activity / transcription elongation factor complex / cytosolic ribosome assembly / regulation of DNA-templated transcription elongation / transcription antitermination / regulation of cell growth / maintenance of translational fidelity / DNA-templated transcription termination / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / 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 / cytoplasmic translation / small ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / transferase activity / tRNA binding / negative regulation of translation / rRNA binding / molecular adaptor activity / ribosome / structural constituent of ribosome / translation / response to antibiotic / mRNA binding / GTPase activity / negative regulation of DNA-templated transcription / GTP binding / protein homodimerization activity / DNA binding / RNA binding / zinc ion binding / membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) Streptomyces (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | |||||||||
Authors | Pulk, A. / Cate, J.H.D. | |||||||||
Citation | Journal: Science / Year: 2013 Title: Control of ribosomal subunit rotation by elongation factor G. Authors: Pulk, A. / 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 | 4v9o.cif.gz | 14.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4v9o.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 4v9o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v9/4v9o ftp://data.pdbj.org/pub/pdb/validation_reports/v9/4v9o | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
-RNA chain , 3 types, 12 molecules ABCBEBGBAACAEAGABADAFAHA
#1: RNA chain | Mass: 38790.090 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: GenBank: AP012306.1 #3: RNA chain | Mass: 941612.375 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: GenBank: AP012306.1 #35: RNA chain | Mass: 499690.031 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: k-12 / References: GenBank: AP012306.1 |
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+50S ribosomal protein ... , 31 types, 120 molecules ACCCECGCADCDEDGDAECEEEGEAFCFEFGFAGCGEGGGAHCHEHGHAICIEIGIAJCJ...
-30S ribosomal protein ... , 20 types, 80 molecules BBDBFBHBBCDCFCHCBDDDFDHDBEDEFEHEBFDFFFHFBGDGFGHGBHDHFHHHBIDI...
#34: Protein | Mass: 26781.670 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: k-12 / References: UniProt: P0A7V0 #36: Protein | Mass: 26031.316 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: k-12 / References: UniProt: P0A7V3 #37: Protein | Mass: 23514.199 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: k-12 / References: UniProt: P0A7V8 #38: Protein | Mass: 17629.398 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: k-12 / References: UniProt: P0A7W1 #39: Protein | Mass: 15727.512 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: k-12 / References: UniProt: P02358 #40: Protein | Mass: 20055.156 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: k-12 / References: UniProt: P02359 #41: Protein | Mass: 14146.557 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: k-12 / References: UniProt: P0A7W7 #42: Protein | Mass: 14886.270 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: k-12 / References: UniProt: P0A7X3 #43: Protein | Mass: 11755.597 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: k-12 / References: UniProt: P0A7R5 #44: Protein | Mass: 13870.975 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: k-12 / References: UniProt: P0A7R9 #45: Protein | Mass: 13768.157 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: k-12 / References: UniProt: P0A7S3 #46: Protein | Mass: 13128.467 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: k-12 / References: UniProt: P0A7S9 #47: Protein | Mass: 11606.560 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: k-12 / References: UniProt: P0AG59 #48: Protein | Mass: 10290.816 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: k-12 / References: UniProt: P0ADZ4 #49: Protein | Mass: 9207.572 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: k-12 / References: UniProt: P0A7T3 #50: Protein | Mass: 9724.491 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: k-12 / References: UniProt: P0AG63 #51: Protein | Mass: 9005.472 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: k-12 / References: UniProt: P0A7T7 #52: Protein | Mass: 10455.355 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: k-12 / References: UniProt: P0A7U3 #53: Protein | Mass: 9708.464 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: k-12 / References: UniProt: P0A7U7 #54: Protein | Mass: 8524.039 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: k-12 / References: UniProt: P68679 |
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-Protein / Protein/peptide , 2 types, 8 molecules BVDVFVHVBWDWFWHW
#55: Protein | Mass: 77676.227 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: fusA / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P0A6M8 #56: Protein/peptide | |
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-Non-polymers , 4 types, 4232 molecules
#57: Chemical | ChemComp-MG / #58: Chemical | ChemComp-ZN / #59: Chemical | ChemComp-GCP / #60: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 20 |
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-Sample preparation
Crystal |
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Crystal grow |
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-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: 1.1 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 2.9→70 Å / Num. obs: 1874109 / % possible obs: 83.7 % / Observed criterion σ(F): 0.84 / Observed criterion σ(I): 0.84 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→70 Å / Occupancy max: 1 / Occupancy min: 0.89 / σ(F): 0.52 Details: Zero B values occur for some waters due to scaling from the use of bulk solvent correction in the refinement
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Displacement parameters | Biso max: 145.13 Å2 / Biso mean: 19.6361 Å2 / Biso min: 0 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→70 Å
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