|Entry||Database: EMDB / ID: 5361|
|Title||New mRNA-tRNA translocation intermediates revealed by cryoEM: Class 2 (unrotated 70S ribosome with A-site and P-site tRNAs)|
|Keywords||ribosome / 70S / unrotated / intermediates / translocation / tRNA|
|Source||Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /|
|Map data||This is the Class 2 with classical tRNAs.|
|Method||single particle reconstruction, at 12.1 Å resolution|
|Authors||Agirrezabala X / Liao HY / Schreiner E / Fu J / Ortiz-Meoz RF / Schulten K / Green R / Frank J|
|Citation||Proc. Natl. Acad. Sci. U.S.A., 2012, 109, 6094-6099|
Proc. Natl. Acad. Sci. U.S.A., 2012, 109, 6094-6099 Yorodumi Papers
|Validation Report||PDB-ID: 4v6n|
SummaryFull reportAbout validation report
|Date||Deposition: Dec 2, 2011 / Header (metadata) release: Jan 26, 2012 / Map release: Feb 16, 2012 / Last update: Jul 23, 2014|
Downloads & links
|File||emd_5361.map.gz (map file in CCP4 format, 61037 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 1.5 Å|
CCP4 map header:
-Entire Trp-tRNA-EFTu-GDP-kir-70S ribosome
|Entire||Name: Trp-tRNA-EFTu-GDP-kir-70S ribosome / Number of components: 3 / Oligomeric State: monomeric|
|Mass||Theoretical: 2.8 MDa / Experimental: 2.8 MDa|
-Component #1: ribosome-prokaryote, 70S ribosome
|Ribosome-prokaryote||Name: 70S ribosome / Prokaryote: ALL / Recombinant expression: No|
|Source||Species: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /|
|Sample solution||Specimen conc.: 0.03 mg/ml|
Buffer solution: HiFi buffer (50 mM Tris-HCl, pH 7.5, 70mM NH4Cl, 30 mM KCl, 3.5 mM MgCl2, 0.5 mM spermidine, 8mM putrescine, 2 mM DTT, 3.5 mM MgCl2)
|Support film||200 mesh|
|Vitrification||Instrument: FEI VITROBOT / Cryogen name: NITROGEN / Temperature: 80 K / Humidity: 90 % / Method: blot for 3 seconds / Details: Vitrification instrument: Vitrobot|
-Electron microscopy imaging
Model: Tecnai F30 / Image courtesy: FEI Company
|Imaging||Microscope: FEI TECNAI F30 / Date: May 1, 2007|
Details: automated data collection system AutoEMation (CCD mag. 100000x)
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 25 e/Å2 / Electron beam tilt params: no tilt / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 59000 X (nominal), 58269 X (calibrated)|
Astigmatism: objective corrected at 100,000 times magnification
Cs: 2.26 mm / Imaging mode: BRIGHT FIELD / Defocus: 1200 - 4000 nm / Energy filter: no filter
|Specimen Holder||Holder: cartridge / Model: OTHER / Temperature: 80.7 K ( 80.7 - 80.7 K)|
|Camera||Detector: TVIPS TEMCAM-F415 (4k x 4k)|
|Processing||Method: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 36000|
|3D reconstruction||Software: XMIPP, SPIDER / CTF correction: defocus groups, Wiener filter / Details: Classification using ML3D / Resolution: 12.1 Å / Resolution method: FSC 0.5|
-Atomic model buiding
|Modeling #1||Software: MDFF / Refinement protocol: flexible / Target criteria: RMSD, cross correlation / Refinement space: REAL|
Details: Protocol: Molecular Dynamics based flexible fitting
Input PDB model: 2I2U
|Modeling #2||Software: MDFF / Refinement protocol: flexible / Target criteria: RMSD, cross correlation / Refinement space: REAL|
Details: Protocol: Molecular Dynamics based flexible fitting
Input PDB model: 2I2V
-Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017
Three pioneers of this field were awarded Nobel Prize in Chemistry 2017
- Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
- Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
- Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.
External links: The 2017 Nobel Prize in Chemistry - Press Release
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