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Yorodumi- EMDB-1499: Structure of the E. coli trigger factor bound to a translating ri... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1499 | |||||||||
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Title | Structure of the E. coli trigger factor bound to a translating ribosome | |||||||||
Map data | Structure of the E. coli trigger factor bound to a translating ribosome | |||||||||
Sample |
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Keywords | trigger factor / ribosome-nascent chain complex / translating ribosome / co-translational protein folding / chaperone | |||||||||
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 / ribosomal large subunit assembly / peptidyl-prolyl cis-trans isomerase activity / protein transport / ribosome binding ...'de novo' cotranslational protein folding / stress response to copper ion / protein unfolding / chaperone-mediated protein folding / protein folding chaperone / peptidylprolyl isomerase / ribosomal large subunit assembly / peptidyl-prolyl cis-trans isomerase activity / protein transport / ribosome binding / large ribosomal subunit rRNA binding / response to heat / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / ribosome / structural constituent of ribosome / translation / cell division / identical protein binding / membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 19.0 Å | |||||||||
Authors | Merz F / Boehringer D / Schaffitzel C / Preissler S / Hoffmann A / Maier T / Rutkowska A / Lozza J / Ban N / Bukau B / Deuerling E | |||||||||
Citation | Journal: EMBO J / Year: 2008 Title: Molecular mechanism and structure of Trigger Factor bound to the translating ribosome. Authors: Frieder Merz / Daniel Boehringer / Christiane Schaffitzel / Steffen Preissler / Anja Hoffmann / Timm Maier / Anna Rutkowska / Jasmin Lozza / Nenad Ban / Bernd Bukau / Elke Deuerling / Abstract: Ribosome-associated chaperone Trigger Factor (TF) initiates folding of newly synthesized proteins in bacteria. Here, we pinpoint by site-specific crosslinking the sequence of molecular interactions ...Ribosome-associated chaperone Trigger Factor (TF) initiates folding of newly synthesized proteins in bacteria. Here, we pinpoint by site-specific crosslinking the sequence of molecular interactions of Escherichia coli TF and nascent chains during translation. Furthermore, we provide the first full-length structure of TF associated with ribosome-nascent chain complexes by using cryo-electron microscopy. In its active state, TF arches over the ribosomal exit tunnel accepting nascent chains in a protective void. The growing nascent chain initially follows a predefined path through the entire interior of TF in an unfolded conformation, and even after folding into a domain it remains accommodated inside the protective cavity of ribosome-bound TF. The adaptability to accept nascent chains of different length and folding states may explain how TF is able to assist co-translational folding of all kinds of nascent polypeptides during ongoing synthesis. Moreover, we suggest a model of how TF's chaperoning function can be coordinated with the co-translational processing and membrane targeting of nascent polypeptides by other ribosome-associated factors. | |||||||||
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_1499.map.gz | 3 MB | EMDB map data format | |
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Header (meta data) | emd-1499-v30.xml emd-1499.xml | 10.6 KB 10.6 KB | Display Display | EMDB header |
Images | 1499.gif | 59.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1499 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1499 | HTTPS FTP |
-Validation report
Summary document | emd_1499_validation.pdf.gz | 253.9 KB | Display | EMDB validaton report |
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Full document | emd_1499_full_validation.pdf.gz | 253.1 KB | Display | |
Data in XML | emd_1499_validation.xml.gz | 5.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1499 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1499 | HTTPS FTP |
-Related structure data
Related structure data | 2vrhMC 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_1499.map.gz / Format: CCP4 / Size: 3.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Structure of the E. coli trigger factor bound to a translating ribosome | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.23333 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 : Escherichia coli Trigger Factor associated with an Escherichia co...
Entire | Name: Escherichia coli Trigger Factor associated with an Escherichia coli ribosome-nascent chain complex |
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Components |
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-Supramolecule #1000: Escherichia coli Trigger Factor associated with an Escherichia co...
Supramolecule | Name: Escherichia coli Trigger Factor associated with an Escherichia coli ribosome-nascent chain complex type: sample / ID: 1000 / Details: monodisperse sample / Number unique components: 2 |
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Molecular weight | Experimental: 2.6 MDa |
-Supramolecule #1: ribosome-nascent chain complex
Supramolecule | Name: ribosome-nascent chain complex / type: complex / ID: 1 / Name.synonym: translating ribosome / Details: SecM-stalled E. coli ribosome complex / Recombinant expression: No / Ribosome-details: ribosome-prokaryote: ALL |
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Source (natural) | Organism: Escherichia coli (E. coli) |
-Macromolecule #1: trigger factor
Macromolecule | Name: trigger factor / type: protein_or_peptide / ID: 1 / Name.synonym: trigger factor Details: trigger factor crosslinked to the nascent chain. Mutant TFS61C E. coli Oligomeric state: monomer / Recombinant expression: No |
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Source (natural) | Organism: Escherichia coli (E. coli) / Strain: mutant TFS61c |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 Details: 50 mM Hepes-KOH pH 7.5, 100 mM KCl, 25 mM MgCl2, 0.5 mg/ml chloramphenicol |
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Vitrification | Cryogen name: ETHANE / Instrument: OTHER |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Temperature | Average: 88 K |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 6.35 µm / Details: rotating-drum scanner |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 50000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder: Side entry liquid nitrogen-cooled cryo specimen holder Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: each image |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 19.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMAGIC-5, SPIDER Details: Final rounds of refinement were done using the Spider software |
-Atomic model buiding 1
Initial model | PDB ID: Chain - Chain ID: A |
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Details | Protocol: Rigid Body. exhaustive search |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross Correlation |
Output model | PDB-2vrh: |