+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2696 | |||||||||
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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 (conformation1) | |||||||||
Sample |
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Keywords | translation / co-translational protein folding | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / negative staining / Resolution: 13.1 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_2696.map.gz | 11 MB | EMDB map data format | |
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Header (meta data) | emd-2696-v30.xml emd-2696.xml | 9.7 KB 9.7 KB | Display Display | EMDB header |
Images | EMD-2696.png | 239 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2696 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2696 | HTTPS FTP |
-Validation report
Summary document | emd_2696_validation.pdf.gz | 243.1 KB | Display | EMDB validaton report |
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Full document | emd_2696_full_validation.pdf.gz | 242.2 KB | Display | |
Data in XML | emd_2696_validation.xml.gz | 6.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2696 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2696 | HTTPS FTP |
-Related 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_2696.map.gz / Format: CCP4 / Size: 94.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | TnaC-stalled RNC with long nascent chain bound to Trigger Factor (conformation1) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 - conformation 1
Entire | Name: TnaC stalled RNC with Trigger factor - conformation 1 |
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Components |
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-Supramolecule #1000: TnaC stalled RNC with Trigger factor - conformation 1
Supramolecule | Name: TnaC stalled RNC with Trigger factor - conformation 1 / 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: 95 % / Instrument: FEI VITROBOT MARK III Method: Blot for 10 seconds before plunging, use 2 layers of filter paper V |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Details | Final magnification of the object on the CCD image is 148721 |
Date | Jun 4, 2012 |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Digitization - Sampling interval: 15.6 µm / Number real images: 13200 / Average electron dose: 20 e/Å2 / Bits/pixel: 16 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 75000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: -3.6 µm / Nominal defocus min: -1.2 µm / Nominal magnification: 75000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / 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: 13.1 Å / Resolution method: OTHER / Software - Name: SPIDER / Details: Filtered to 13.1 Angstrom / Number images used: 100931 |