|Entry||Database: PDB / ID: 4urd|
|Title||Cryo-EM map of Trigger Factor bound to a translating ribosome|
|Keywords||ISOMERASE / 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 / ribosome binding / protein transport / response to heat / cell cycle / cell division / membrane / identical protein binding / cytosol / un:i4uk46: / Trigger factor|
Function and homology information
|Specimen source||ESCHERICHIA COLI (E. coli)|
|Method||ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 7.7 Å resolution|
|Authors||Deeng, J. / Chan, K.Y. / 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.
SummaryFull reportAbout validation report
|Date||Deposition: Jun 27, 2014 / Release: Jan 13, 2016|
|Structure viewer||Molecule: |
Downloads & links
A: TRIGGER FACTOR
|#1: Protein/peptide|| |
Mass: 12711.546 Da / Num. of mol.: 1 / Fragment: RIBOSOME BINDING DOMAIN, RESIDUES 1-115 / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: I4UK46, UniProt: P0A850*PLUS
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: PARTICLE / Reconstruction method: single particle reconstruction|
|Component||Name: TNAC-STALLED-RNC WITH TRIGGER FACTOR / Type: COMPLEX|
|Buffer solution||Name: 20 MM HEPES, 100 MM KOAC, 10 MM MG(OAC)2, 2 MM DTT / Details: 20 MM HEPES, 100 MM KOAC, 10 MM MG(OAC)2, 2 MM DTT / pH: 7.4|
|Specimen||Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES|
|Specimen support||Details: HOLEY CARBON|
|Vitrification||Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE|
Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, INSTRUMENT- FEI VITROBOT MARK III, METHOD- BLOT FOR 10 SECONDS BEFORE PLUNGING, USE 2 LAYERS OF FILTER PAPER V,
-Electron microscopy imaging
Model: Tecnai F30 / Image courtesy: FEI Company
|Microscopy||Microscope model: FEI TECNAI F30 / Date: Nov 21, 2010|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM|
|Electron lens||Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 39000 / Calibrated magnification: 38900 / Nominal defocus max: 3500 nm / Nominal defocus min: 1200 nm / Cs: 2 mm|
|Image recording||Electron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM|
|Image scans||Number digital images: 221|
|EM software||Name: SPIDER / Category: 3D reconstruction|
|CTF correction||Details: ON VOLUMES (SPIDER)|
|Symmetry||Point symmetry: C1|
|3D reconstruction||Method: PROJECTION MATCHING / Resolution: 7.7 Å / Number of particles: 100931|
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2695. (DEPOSITION ID: 12641).
Symmetry type: POINT
|Least-squares process||Highest resolution: 7.7 Å|
|Refine hist #LAST||Highest resolution: 7.7 Å|
|Number of atoms included #LAST||Protein: 893 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 893|
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