+Open data
-Basic information
Entry | Database: PDB / ID: 4v69 | |||||||||
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Title | Ternary complex-bound E.coli 70S ribosome. | |||||||||
Components |
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Keywords | RIBOSOME / ternary complex / flexible fitting / cryo-EM / 30S / 50S / tRNA / mRNA / EF-Tu / 70S / Ribonucleoprotein / Ribosomal protein / RNA-binding / rRNA-binding / Antibiotic resistance / Repressor / Transcription / Transcription regulation / Transcription termination / Translation regulation / tRNA-binding / Methylation / Endonuclease / Hydrolase / Nuclease / Cell membrane / Elongation factor / GTP-binding / Membrane / Nucleotide-binding / Phosphoprotein / Protein biosynthesis | |||||||||
Function / homology | Function and homology information guanyl-nucleotide exchange factor complex / guanosine tetraphosphate binding / stringent response / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / translational elongation / RNA folding / transcriptional attenuation ...guanyl-nucleotide exchange factor complex / guanosine tetraphosphate binding / stringent response / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / translational elongation / 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 / 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 / GTPase activity / mRNA binding / GTP binding / DNA binding / RNA binding / zinc ion binding / membrane / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.7 Å | |||||||||
Authors | Villa, E. / Sengupta, J. / Trabuco, L.G. / LeBarron, J. / Baxter, W.T. / Shaikh, T.R. / Grassucci, R.A. / Nissen, P. / Ehrenberg, M. / Schulten, K. / Frank, J. | |||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2009 Title: Ribosome-induced changes in elongation factor Tu conformation control GTP hydrolysis. Authors: Elizabeth Villa / Jayati Sengupta / Leonardo G Trabuco / Jamie LeBarron / William T Baxter / Tanvir R Shaikh / Robert A Grassucci / Poul Nissen / Måns Ehrenberg / Klaus Schulten / Joachim Frank / Abstract: In translation, elongation factor Tu (EF-Tu) molecules deliver aminoacyl-tRNAs to the mRNA-programmed ribosome. The GTPase activity of EF-Tu is triggered by ribosome-induced conformational changes of ...In translation, elongation factor Tu (EF-Tu) molecules deliver aminoacyl-tRNAs to the mRNA-programmed ribosome. The GTPase activity of EF-Tu is triggered by ribosome-induced conformational changes of the factor that play a pivotal role in the selection of the cognate aminoacyl-tRNAs. We present a 6.7-A cryo-electron microscopy map of the aminoacyl-tRNA x EF-Tu x GDP x kirromycin-bound Escherichia coli ribosome, together with an atomic model of the complex obtained through molecular dynamics flexible fitting. The model reveals the conformational changes in the conserved GTPase switch regions of EF-Tu that trigger hydrolysis of GTP, along with key interactions, including those between the sarcin-ricin loop and the P loop of EF-Tu, and between the effector loop of EF-Tu and a conserved region of the 16S rRNA. Our data suggest that GTP hydrolysis on EF-Tu is controlled through a hydrophobic gate mechanism. #1: Journal: Structure / Year: 2008 Title: Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics. Authors: Trabuco, L. / Villa, E. / Mitra, K. / Frank, J. / Schulten, K. #2: Journal: J.Struct.Biol. / Year: 2008 Title: Exploration of parameters in cryo-EM leading to an improved density map of the E. coli ribosome Authors: LeBarron, J. / Grassucci, R.A. / Shaikh, T.R. / Baxter, W.T. / Sengupta, J. / Frank, J. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 4v69.cif.gz | 3.8 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4v69.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 4v69.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4v69_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 4v69_full_validation.pdf.gz | 6.2 MB | Display | |
Data in XML | 4v69_validation.xml.gz | 707.1 KB | Display | |
Data in CIF | 4v69_validation.cif.gz | 979.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v6/4v69 ftp://data.pdbj.org/pub/pdb/validation_reports/v6/4v69 | HTTPS FTP |
-Related structure data
Related structure data | 5036MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-30S ribosomal protein ... , 20 types, 20 molecules AJAKALAMANAOAPAQARASATAUABACADAEAFAGAHAI
#1: Protein | Mass: 11196.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7R5 |
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#2: Protein | Mass: 12487.200 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7R9 |
#3: Protein | Mass: 13636.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7S3 |
#4: Protein | Mass: 12528.639 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7S9 |
#5: Protein | Mass: 11028.997 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AG59 |
#6: Protein | Mass: 10188.687 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: Q8X9M2 |
#7: Protein | Mass: 9065.417 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7T3 |
#8: Protein | Mass: 9263.946 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AG63 |
#9: Protein | Mass: 6466.477 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7T7 |
#10: Protein | Mass: 9057.626 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7U3 |
#11: Protein | Mass: 9506.190 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7U7 |
#12: Protein | Mass: 6067.081 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P68679 |
#13: Protein | Mass: 24253.943 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7V0 |
#14: Protein | Mass: 23078.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7V3 |
#15: Protein | Mass: 23383.002 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7V8 |
#16: Protein | Mass: 15804.282 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7W1 |
#17: Protein | Mass: 11669.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P02358 |
#18: Protein | Mass: 16764.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P02359 |
#19: Protein | Mass: 14015.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7W7 |
#20: Protein | Mass: 14554.882 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7X3 |
-RNA chain , 7 types, 7 molecules AAAYAWAXAVBBBA
#21: RNA chain | Mass: 495927.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 83754040 |
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#22: RNA chain | Mass: 24518.570 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in yeast. |
#23: RNA chain | Mass: 24485.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) |
#24: RNA chain | Mass: 3499.162 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: mRNA was synthetically contstructed |
#26: RNA chain | Mass: 24816.811 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) |
#57: RNA chain | Mass: 941306.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 33357927 |
#58: RNA chain | Mass: 37848.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 33357928 |
+50S ribosomal protein ... , 30 types, 30 molecules B5BIBJBKBLBMBNBOBPBQBRBSBTBUBVBWBXBYBCBZB0B1B2B3B4BDBEBFBGBH
-Protein / Non-polymers , 2 types, 2 molecules AZ
#25: Protein | Mass: 43239.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A6N1, UniProt: P0CE48*PLUS |
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#59: Chemical | ChemComp-GDP / |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: E. coli ribosome in complex with the ternary complex EF-Tu aminoacyl-tRNA GDP Type: RIBOSOME |
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Buffer solution | pH: 7.5 |
Specimen | Conc.: 0.0768 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: Thin carbon on 300 mesh Quantifoil R2/4 |
Vitrification | Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE Details: Vitrification using FEI Vitrobot; blot 3 seconds before plunging with an offset of -1mm |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
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Microscopy | Model: FEI POLARA 300 / Date: Aug 31, 2006 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 59000 X / Calibrated magnification: 58279 X / Nominal defocus max: 1200 nm / Nominal defocus min: 4520 nm |
Specimen holder | Temperature: 84 K |
Image recording | Electron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
-Processing
EM software |
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CTF correction | Details: Correction of reconstruction of each defocus group | |||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 6.7 Å / Num. of particles: 131599 / Actual pixel size: 1.2 Å / Details: see LeBarron et al., JSB 164 (2008) 24-32. / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL Target criteria: Cross correlation, root-mean square deviation Details: METHOD--See Trabuco et al., Structure 16 (2008) 673-683. REFINEMENT PROTOCOL--Flexible fitting | |||||||||||||||||||||||||||||||||||
Atomic model building |
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Refinement step | Cycle: LAST
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