|Entry||Database: EMDB / ID: 6171|
|Title||Electron cryo-microscopy of peptidyl-tRNA bound to yeast 60S ribosome|
|Keywords||ribosome quality control complex / RQC / eukaryotic ribosome rescue / stalled nascent chain|
|Sample||RQC particles purified by co-IP of Rqc1-FLAG, eluted with 3xFLAG peptide|
|Source||Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /|
|Map data||structure of peptidyl-tRNA-60S, related to Fig. 1A of the primary citation. For the masked, sharpened map, see EMD-6201|
|Method||single particle reconstruction, at 5.9 Å resolution|
|Authors||Shen PS / Park J / Qin Y / Li X / Parsawar K / Larson M / Cox J / Cheng Y / Lambowitz AM / Weissman JS / Brandman O / Frost A|
|Citation||Science, 2015, 347, 75-78|
Science, 2015, 347, 75-78 Yorodumi Papers
|Date||Deposition: Nov 4, 2014 / Header (metadata) release: Dec 24, 2014 / Map release: Jan 7, 2015 / Last update: Jan 21, 2015|
Downloads & links
|File||emd_6171.map.gz (map file in CCP4 format, 289408 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 1.22 Å|
CCP4 map header:
-Entire RQC particles purified by co-IP of Rqc1-FLAG, eluted with 3xFLAG ...
|Entire||Name: RQC particles purified by co-IP of Rqc1-FLAG, eluted with 3xFLAG peptide|
Details: RQC particles were 3D classified to reveal distinct subclasses containing various RQC components.
Number of components: 1
-Component #1: ribosome-eukaryote, 60S ribosome
|Ribosome-eukaryote||Name: 60S ribosome / a.k.a: large ribosomal subunit / Eukaryote: LSU 60S, LSU RNA 28S, LSU RNA 5.8S, LSU RNA 5S / Recombinant expression: No|
|Source||Species: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ / |
|Sample solution||Buffer solution: 100 mM KOAc, 10 mM MgCl2, 25 mM HEPES-KOH / pH: 7.4|
|Support film||200 mesh Quantifoil R2/2 grid + lacey carbon grid with ultrathin carbon|
|Vitrification||Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Temperature: 90 K / Humidity: 75 % / Method: Blot for 3 seconds before plunging|
-Electron microscopy imaging
Model: Tecnai Polara / Image courtesy: FEI Company
|Imaging||Microscope: FEI POLARA 300 / Date: Jul 22, 2013 / Details: UCSF Image4 on-the-fly motion correction|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 35 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 31000 X (nominal) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 800 - 2000 nm / Energy filter: Gatan|
|Specimen Holder||Holder: LN2 cooled / Model: GATAN LIQUID NITROGEN / Temperature: 85 K ( 80 - 90 K)|
|Camera||Detector: GATAN K2 (4k x 4k)|
|Image acquisition||Number of digital images: 3459 / Bit depth: 8|
|Processing||Method: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 29956|
Details: Particles were selected using the semi-automated swarm tool in e2boxer.py of the EMAN2 package. All 2D and 3D processing was performed in RELION.
|3D reconstruction||Software: RELION, CTFFIND3 / CTF correction: each particle|
Details: Unmasked map related to Fig. 1A of the primary citation. For the masked, sharpened map, see EMD-6201
Resolution: 5.9 Å / Resolution method: FSC 0.143, gold-standard
-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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