+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2695 | |||||||||
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Title | Cryo-EM map of Trigger Factor bound to a translating ribosome | |||||||||
Map data | High resolution map of ribosome-bound Trigger Factor | |||||||||
Sample |
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Keywords | translation / co-translational protein folding | |||||||||
Function / homology | Function and homology information 'de novo' cotranslational protein folding / stress response to copper ion / protein unfolding / chaperone-mediated protein folding / protein folding chaperone / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein transport / ribosome binding / response to heat ...'de novo' cotranslational protein folding / stress response to copper ion / protein unfolding / chaperone-mediated protein folding / protein folding chaperone / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein transport / ribosome binding / response to heat / cell division / identical protein binding / membrane / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / negative staining / Resolution: 7.7 Å | |||||||||
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. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_2695.map.gz | 17.3 MB | EMDB map data format | |
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Header (meta data) | emd-2695-v30.xml emd-2695.xml | 9.8 KB 9.8 KB | Display Display | EMDB header |
Images | EMD-2695.png | 339 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2695 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2695 | HTTPS FTP |
-Validation report
Summary document | emd_2695_validation.pdf.gz | 301.4 KB | Display | EMDB validaton report |
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Full document | emd_2695_full_validation.pdf.gz | 300.5 KB | Display | |
Data in XML | emd_2695_validation.xml.gz | 6.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2695 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2695 | HTTPS FTP |
-Related structure data
Related structure data | 4urdMC 2696C 2711C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_2695.map.gz / Format: CCP4 / Size: 94.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | High resolution map of ribosome-bound Trigger Factor | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.2375 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : TnaC-stalled-RNC with Trigger factor
Entire | Name: TnaC-stalled-RNC with Trigger factor |
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Components |
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-Supramolecule #1000: TnaC-stalled-RNC with Trigger factor
Supramolecule | Name: TnaC-stalled-RNC with Trigger factor / type: sample / ID: 1000 / Oligomeric state: monomer / Number unique components: 2 |
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-Supramolecule #1: cytosolic 70S ribosome
Supramolecule | Name: cytosolic 70S ribosome / type: complex / ID: 1 / Name.synonym: 70S / Recombinant expression: No / Ribosome-details: ribosome-prokaryote: ALL |
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Source (natural) | Organism: Escherichia coli (E. coli) / Strain: KC6 |
-Macromolecule #1: Trigger factor
Macromolecule | Name: Trigger factor / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Oligomeric state: 1 / Recombinant expression: Yes |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Experimental: 48 KDa / Theoretical: 48 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 / Details: 20 mM HEPES, 100 mM KOAc, 10 mM Mg(OAc)2, 2 mM DTT |
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Staining | Type: NEGATIVE / Details: Cryo-EM |
Grid | Details: Quantifoil R3/3 holey carbon supported grids |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK III Method: Blot for 10 seconds before plunging, use 2 layers of filter paper V |
-Electron microscopy
Microscope | FEI TECNAI F30 |
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Date | Nov 21, 2010 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 4.35 µm / Number real images: 221 / Average electron dose: 20 e/Å2 / Od range: 1.2 / Bits/pixel: 16 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 38900 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: -3.5 µm / Nominal defocus min: -1.2 µm / Nominal magnification: 39000 |
Sample stage | Specimen holder model: OTHER |
Experimental equipment | Model: Tecnai F30 / Image courtesy: FEI Company |
-Image processing
Details | The particles were selected using SIGNATURE and processed using SPIDER |
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CTF correction | Details: on volumes (SPIDER) |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 7.7 Å / Resolution method: OTHER / Software - Name: SPIDER / Number images used: 100931 |