|Entry||Database: EMDB / ID: 2695|
|Title||Cryo-EM map of Trigger Factor bound to a translating ribosome|
|Map data||High resolution map of ribosome-bound Trigger Factor|
|Sample||TnaC-stalled-RNC with Trigger factor:|
ribosome-prokaryote / Trigger factor
|Keywords||translation / co-translational protein folding|
|Function / homology||Trigger factor / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / Bacterial trigger factor protein (TF) C-terminus / Bacterial trigger factor protein (TF) / FKBP-type peptidyl-prolyl cis-trans isomerase / Trigger factor, C-terminal domain superfamily / Trigger factor ribosome-binding domain superfamily / Trigger factor/SurA domain superfamily / Trigger factor, ribosome-binding, bacterial / Trigger factor, C-terminal ...Trigger factor / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / Bacterial trigger factor protein (TF) C-terminus / Bacterial trigger factor protein (TF) / FKBP-type peptidyl-prolyl cis-trans isomerase / Trigger factor, C-terminal domain superfamily / Trigger factor ribosome-binding domain superfamily / Trigger factor/SurA domain superfamily / Trigger factor, ribosome-binding, bacterial / Trigger factor, C-terminal / FKBP-type peptidyl-prolyl cis-trans isomerase domain / 'de novo' cotranslational protein folding / protein folding chaperone / protein unfolding / chaperone-mediated protein folding / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein transport / ribosome binding / response to heat / cell cycle / cell division / membrane / identical protein binding / cytosol / un:i4uk46: / Trigger factor|
Function and homology information
|Source||Escherichia coli (E. coli)|
|Method||single particle reconstruction / cryo EM / 7.7 Å resolution|
|Authors||Deeng J / Chan KY / van der Sluis E / Bischoff L / Berninghausen O / Han W / Gumbart J / Schulten K / Beatrix B / Beckmann R|
|Citation||Journal: J. Mol. Biol. / Year: 2016|
Title: Dynamic Behavior of Trigger Factor on the Ribosome.
Authors: J Deeng / K Y Chan / E O van der Sluis / O Berninghausen / W Han / J Gumbart / K Schulten / B Beatrix / R Beckmann
Abstract: Trigger factor (TF) is the only ribosome-associated chaperone in bacteria. It interacts with hydrophobic segments in nascent chain (NCs) as they emerge from the ribosome. TF binds via its N-terminal ...Trigger factor (TF) is the only ribosome-associated chaperone in bacteria. It interacts with hydrophobic segments in nascent chain (NCs) as they emerge from the ribosome. TF binds via its N-terminal ribosome-binding domain (RBD) mainly to ribosomal protein uL23 at the tunnel exit on the large ribosomal subunit. Whereas earlier structural data suggested that TF binds as a rigid molecule to the ribosome, recent comparisons of structural data on substrate-bound, ribosome-bound, and TF in solution from different species suggest that this chaperone is a rather flexible molecule. Here, we present two cryo-electron microscopy structures of TF bound to ribosomes translating an mRNA coding for a known TF substrate from Escherichia coli of a different length. The structures reveal distinct degrees of flexibility for the different TF domains, a conformational rearrangement of the RBD upon ribosome binding, and an increase in rigidity within TF when the NC is extended. Molecular dynamics simulations agree with these data and offer a molecular basis for these observations.
|Validation Report||PDB-ID: 4urd|
SummaryFull reportAbout validation report
|Date||Deposition: Jun 27, 2014 / Header (metadata) release: Aug 6, 2014 / Map release: Jul 15, 2015 / Last update: Sep 28, 2016|
|Structure viewer||EM map: |
Downloads & links
|File||emd_2695.map.gz (map file in CCP4 format, 99268 KB)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.2375 Å|
CCP4 map header:
-Entire TnaC-stalled-RNC with Trigger factor
|Entire||Name: TnaC-stalled-RNC with Trigger factor / Number of components: 2 / Oligomeric State: monomer|
-Component #1: ribosome-prokaryote, cytosolic 70S ribosome
|Ribosome-prokaryote||Name: cytosolic 70S ribosome / a.k.a: 70S / Prokaryote: ALL / Recombinant expression: No|
|Source||Species: Escherichia coli (E. coli) / Strain: KC6|
-Component #2: protein, Trigger factor
|Protein||Name: Trigger factor / Oligomeric Details: 1 / Recombinant expression: Yes / Number of Copies: 1|
|Mass||Theoretical: 48 kDa / Experimental: 48 kDa|
|Source||Species: Escherichia coli (E. coli)|
|Source (engineered)||Expression System: Escherichia coli (E. coli)|
|Specimen||Specimen state: particle / Method: cryo EM|
|Sample solution||Buffer solution: 20 mM HEPES, 100 mM KOAc, 10 mM Mg(OAc)2, 2 mM DTT|
|Support film||Quantifoil R3/3 holey carbon supported grids|
|Vitrification||Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 %|
Method: Blot for 10 seconds before plunging, use 2 layers of filter paper V
-Electron microscopy imaging
Model: Tecnai F30 / Image courtesy: FEI Company
|Imaging||Microscope: FEI TECNAI F30 / Date: Nov 21, 2010|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 20 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 39000 X (nominal), 38900 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: -1200 - -3500 nm|
|Specimen Holder||Model: OTHER|
|Camera||Detector: KODAK SO-163 FILM|
|Image acquisition||Number of digital images: 221 / Scanner: OTHER / Sampling size: 4.35 microns / Bit depth: 16 / OD range: 1.2|
|Processing||Method: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 100931|
Details: The particles were selected using SIGNATURE and processed using SPIDER
|3D reconstruction||Algorithm: Projection Matching / Software: SPIDER / CTF correction: on volumes (SPIDER) / Resolution: 7.7 Å / Resolution method: FSC 0.5, semi-independent|
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