|Entry||Database: EMDB / ID: EMD-3901|
|Title||Polyproline-stalled ribosome with distorted A-site and P-site tRNA|
|Sample||Polyproline stalled ribosome with distorted A+P-site tRNA|
|Biological species||Escherichia coli (E. coli)|
|Method||single particle reconstruction / cryo EM / Resolution: 3.9 Å|
|Authors||Huter P / Arenz S / Wilson DN|
|Citation||Journal: Mol Cell / Year: 2017|
Title: Structural Basis for Polyproline-Mediated Ribosome Stalling and Rescue by the Translation Elongation Factor EF-P.
Authors: Paul Huter / Stefan Arenz / Lars V Bock / Michael Graf / Jan Ole Frister / Andre Heuer / Lauri Peil / Agata L Starosta / Ingo Wohlgemuth / Frank Peske / Jiří Nováček / Otto Berninghausen ...Authors: Paul Huter / Stefan Arenz / Lars V Bock / Michael Graf / Jan Ole Frister / Andre Heuer / Lauri Peil / Agata L Starosta / Ingo Wohlgemuth / Frank Peske / Jiří Nováček / Otto Berninghausen / Helmut Grubmüller / Tanel Tenson / Roland Beckmann / Marina V Rodnina / Andrea C Vaiana / Daniel N Wilson /
Abstract: Ribosomes synthesizing proteins containing consecutive proline residues become stalled and require rescue via the action of uniquely modified translation elongation factors, EF-P in bacteria, or ...Ribosomes synthesizing proteins containing consecutive proline residues become stalled and require rescue via the action of uniquely modified translation elongation factors, EF-P in bacteria, or archaeal/eukaryotic a/eIF5A. To date, no structures exist of EF-P or eIF5A in complex with translating ribosomes stalled at polyproline stretches, and thus structural insight into how EF-P/eIF5A rescue these arrested ribosomes has been lacking. Here we present cryo-EM structures of ribosomes stalled on proline stretches, without and with modified EF-P. The structures suggest that the favored conformation of the polyproline-containing nascent chain is incompatible with the peptide exit tunnel of the ribosome and leads to destabilization of the peptidyl-tRNA. Binding of EF-P stabilizes the P-site tRNA, particularly via interactions between its modification and the CCA end, thereby enforcing an alternative conformation of the polyproline-containing nascent chain, which allows a favorable substrate geometry for peptide bond formation.
|Validation Report||Summary, Full report, XML, About validation report|
|Structure viewer||EM map: |
Downloads & links
|File||Download / File: emd_3901.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.064 Å|
|Symmetry||Space group: 1|
CCP4 map header:
-Entire Polyproline stalled ribosome with distorted A+P-site tRNA
|Entire||Name: Polyproline stalled ribosome with distorted A+P-site tRNA|
Number of components: 1
-Component #1: protein, Polyproline stalled ribosome with distorted A+P-site tRNA
|Protein||Name: Polyproline stalled ribosome with distorted A+P-site tRNA|
Recombinant expression: No
|Mass||Theoretical: 3 MDa|
|Source||Species: Escherichia coli (E. coli)|
|Specimen||Specimen state: Particle / Method: cryo EM|
|Sample solution||pH: 7.4|
|Vitrification||Cryogen name: ETHANE|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 28 e/Å2 / Illumination mode: SPOT SCAN|
|Lens||Imaging mode: BRIGHT FIELD|
|Specimen Holder||Model: OTHER|
|Camera||Detector: FEI FALCON II (4k x 4k)|
|Processing||Method: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 21128|
|3D reconstruction||Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF|
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