|Entry||Database: EMDB / ID: 6171|
|Title||Electron cryo-microscopy of peptidyl-tRNA bound to yeast 60S ribosome|
|Map data||structure of peptidyl-tRNA-60S, related to Fig. 1A of the primary citation. For the masked, sharpened map, see EMD-6201|
|Sample||RQC particles purified by co-IP of Rqc1-FLAG, eluted with 3xFLAG peptide:|
|Keywords||ribosome quality control complex / RQC / eukaryotic ribosome rescue / stalled nascent chain|
|Source||Saccharomyces cerevisiae (baker's yeast)|
|Method||single particle reconstruction / cryo EM / 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||Journal: Science / Year: 2015|
Title: Protein synthesis. Rqc2p and 60S ribosomal subunits mediate mRNA-independent elongation of nascent chains.
Authors: Peter S Shen / Joseph Park / Yidan Qin / Xueming Li / Krishna Parsawar / Matthew H Larson / James Cox / Yifan Cheng / Alan M Lambowitz / Jonathan S Weissman / Onn Brandman / Adam Frost
Abstract: In Eukarya, stalled translation induces 40S dissociation and recruitment of the ribosome quality control complex (RQC) to the 60S subunit, which mediates nascent chain degradation. Here we report ...In Eukarya, stalled translation induces 40S dissociation and recruitment of the ribosome quality control complex (RQC) to the 60S subunit, which mediates nascent chain degradation. Here we report cryo-electron microscopy structures revealing that the RQC components Rqc2p (YPL009C/Tae2) and Ltn1p (YMR247C/Rkr1) bind to the 60S subunit at sites exposed after 40S dissociation, placing the Ltn1p RING (Really Interesting New Gene) domain near the exit channel and Rqc2p over the P-site transfer RNA (tRNA). We further demonstrate that Rqc2p recruits alanine- and threonine-charged tRNA to the A site and directs the elongation of nascent chains independently of mRNA or 40S subunits. Our work uncovers an unexpected mechanism of protein synthesis, in which a protein--not an mRNA--determines tRNA recruitment and the tagging of nascent chains with carboxy-terminal Ala and Thr extensions ("CAT tails").
|Date||Deposition: Nov 4, 2014 / Header (metadata) release: Dec 24, 2014 / Map release: Jan 7, 2015 / Last update: Jan 21, 2015|
|Structure viewer||EM map: |
Downloads & links
|File||emd_6171.map.gz (map file in CCP4 format, 289408 KB)|
|Projections & slices|
Images are generated by Spider.
|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 (baker's yeast) / Strain: BY4741|
|Specimen||Specimen state: particle / Method: cryo EM|
|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
-Jul 12, 2017. Major update of PDB
Major update of PDB
- wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
- In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.
-Jun 16, 2017. Omokage search with filter
Omokage search with filter
- Result of Omokage search can be filtered by keywords and the database types
Related info.: Omokage search
+Sep 15, 2016. EM Navigator & Yorodumi renewed
EM Navigator & Yorodumi renewed
- New versions of EM Navigator and Yorodumi started
Related info.: Changes in new EM Navigator and Yorodumi
+Aug 31, 2016. New EM Navigator & Yorodumi
New EM Navigator & Yorodumi
- In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
- Current version will continue as 'legacy version' for some time.
Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi
+Apr 13, 2016. Omokage search got faster
Omokage search got faster
- The computation time became ~1/2 compared to the previous version by re-optimization of data accession
- Enjoy "shape similarity" of biomolecules, more!
Related info.: Omokage search
Thousand views of thousand structures
- Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
- This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi