|Entry||Database: EMDB / ID: 2711|
|Title||Cryo-EM map of Trigger Factor bound to a translating ribosome|
|Map data||TnaC-stalled RNC with long nascent chain bound to Trigger Factor (conformation 2)|
|Sample||TnaC stalled RNC with Trigger factor - conformation 2:|
ribosome-prokaryote / Trigger factor
|Keywords||translation / co-translational protein folding|
|Source||Escherichia coli (E. coli)|
|Method||single particle reconstruction / cryo EM / 13.1 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.
|Date||Deposition: Jul 14, 2014 / Header (metadata) release: Aug 27, 2014 / Map release: Aug 12, 2015 / Last update: Sep 28, 2016|
|Structure viewer||EM map: |
Downloads & links
|File||emd_2711.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 - conformation 2
|Entire||Name: TnaC stalled RNC with Trigger factor - conformation 2 / 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: 95 %|
Method: Blot for 10 seconds before plunging, use 2 layers of filter paper V
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS / Date: Jun 4, 2012|
Details: Final magnification of the object on the CCD image is 148721
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 20 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 75000 X (nominal), 75000 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: -1200 - -3600 nm|
|Specimen Holder||Model: FEI TITAN KRIOS AUTOGRID HOLDER|
|Camera||Detector: TVIPS TEMCAM-F416 (4k x 4k)|
|Image acquisition||Number of digital images: 13200 / Sampling size: 15.6 microns / Bit depth: 16|
|Processing||Method: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 72968|
Details: The particles were selected using SIGNATURE and processed using SPIDER
|3D reconstruction||Algorithm: Projection Matching / Software: SPIDER / CTF correction: on volumes (SPIDER) / Details: Filtered to 13.1 Angstrom / Resolution: 13.1 Å / Resolution method: FSC 0.5, semi-independent|
-Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
- The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
- The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.: Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator
-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
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