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- EMDB-5036: Aminoacyl-tRNA-EF-Tu-GDP-kir ternary complex-bound E. coli 70S ri... -
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Open data
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Basic information
Entry | Database: EMDB / ID: 5036 |
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Title | Aminoacyl-tRNA-EF-Tu-GDP-kir ternary complex-bound E. coli 70S ribosome |
![]() | Ternary complex-bound 70S E. coli ribosome |
![]() | 70S ribosome from E. coli complex 70S-fMet-tRNA-Phe-tRNA-EF-Tu-GDP-kirromycin.![]() ribosome-prokaryote / (nucleic-acid ![]() ![]() |
![]() | decoding / tRNA selection / ![]() ![]() ![]() ![]() ![]() |
Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
Source | ![]() ![]() ![]() |
Method | ![]() ![]() |
![]() | Villa E / Sengupta J / Trabuco LG / LeBarron J / Baxter WT / Shaikh TR / Grassucci RA / Nissen P / Ehrenberg M / Schulten K / Frank J |
![]() | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2009 Title: Ribosome-induced changes in elongation factor Tu conformation control GTP hydrolysis. ![]() #1: Journal: J. Struct. Biol. / Year: 2008 Title: Exploration of parameters in cryo-EM leading to an improved density map of the E. coli ribosome. ![]() #2: Journal: Structure / Year: 2008 Title: Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics. ![]() |
Validation Report | PDB-ID: 4v69![]() ![]() ![]() |
Date | Deposition: Dec 1, 2008 / Header (metadata) release: Feb 25, 2009 / Map release: May 5, 2009 / Last update: Jul 23, 2014 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
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Download
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Header (meta data in XML format) | ![]() ![]() ![]() |
Images | ![]() |
FTP directory | ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5036 |
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Links
-Related structure data
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
+Entire 70S ribosome from E. coli complex 70S-fMet-tRNA-Phe-tRNA-EF-Tu-GD...
+Component #1: ribosome-prokaryote, 70S ribosome
+Component #2: nucleic-acid, fMet-tRNAfMet
+Component #3: nucleic-acid, Phe-tRNAPhe
+Component #4: nucleic-acid, tRNA
+Component #5: protein, Elongation factor Tu
-Experimental details
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Sample preparation
Specimen | Specimen state: particle / Method: ![]() |
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Sample solution | Specimen conc.: 0.0768 mg/ml Buffer solution: 5 mM potassium phosphate, 5 mM magnesium acetate, 5 mM ammonium chloride, 95 mM potassium chloride, 0.5 mM calcium chloride, 8 mM putrescine, 1 mM spermidine, and 1 mM dithioerythritol pH: 7.5 |
Support film | Thin Carbon on 300 mesh Quantifoil R2/4 |
Vitrification | Instrument: FEI VITROBOT / Cryogen name: ETHANE / Temperature: 80 K / Humidity: 90 % / Method: Blot 3 seconds before plunging Details: Vitrification instrument: FEI vitrobot. Blot Offset at -1 mm |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Tecnai Polara / Image courtesy: FEI Company |
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![]() | Microscope: FEI POLARA 300 / Date: Aug 31, 2006 / Details: Low dose |
Electron gun | Electron source: FIELD EMISSION GUN![]() |
Lens | Magnification: 59000 X (nominal), 58279 X (calibrated) Astigmatism: Objective lens astigmatism was corrected at 115,000 times magnification with fastscan ccd Cs: 2.26 mm / Imaging mode: BRIGHT FIELD ![]() |
Specimen Holder | Holder: FEI Polara Cartridge / Model: OTHER / Temperature: 84 K |
Camera | Detector: KODAK SO-163 FILM |
-Image acquisition
Image acquisition | Number of digital images: 304 / Scanner: ZEISS SCAI / Sampling size: 7 microns / Bit depth: 12 / OD range: 1.2 |
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Image processing
![]() | Method: ![]() |
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3D reconstruction | Algorithm: weighted back projection / Software: Spider CTF correction: Correction of reconstruction of each defocus group Resolution: 6.7 Å Resolution method: FCS at 0.5 cut-off criterion, extrapolated to full dataset |
-Atomic model buiding
Modeling #1 | Software: MDFF / Refinement protocol: flexible / Target criteria: RMSD, cross correlation / Refinement space: REAL Details: Protocol: MDFF. An atomic model of the entire ribosome and factors was creating using molecular dynamics flexible fitting (Trabuco et al. Flexible Fitting of Atomic Structures into Electron Microscopy Maps Using Molecular Dynamics. Structure (2008) vol. 16 (5) pp. 673-683) Input PDB model: 2I2U |
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Modeling #2 | Software: MDFF / Refinement protocol: flexible / Target criteria: RMSD, cross correlation / Refinement space: REAL Details: Protocol: MDFF. An atomic model of the entire ribosome and factors was creating using molecular dynamics flexible fitting (Trabuco et al. Flexible Fitting of Atomic Structures into Electron Microscopy Maps Using Molecular Dynamics. Structure (2008) vol. 16 (5) pp. 673-683) Input PDB model: 2I2V |
Modeling #3 | Software: MDFF / Refinement protocol: flexible / Target criteria: RMSD, cross correlation / Refinement space: REAL Details: Protocol: MDFF. An atomic model of the entire ribosome and factors was creating using molecular dynamics flexible fitting (Trabuco et al. Flexible Fitting of Atomic Structures into Electron Microscopy Maps Using Molecular Dynamics. Structure (2008) vol. 16 (5) pp. 673-683) Input PDB model: 1OB2 |
Output model |