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Structure of the E. coli trigger factor bound to a translating ribosome
by single particle reconstruction, at 19 A resolution
#1: Surface view with section colored by density value, Surface level: 200, Made by UCSF CHIMERA
#2: Surface view colored by height, Surface level: 200, Made by UCSF CHIMERA
#3: Surface view with fitted model, atomic models: PDB-2vrh, Surface level: 200, Made by UCSF CHIMERA
#4: Simplified surface model with fitted atomic model: PDB-2vrh, Made by Jmol
 Entry | |
| Summary | |
| Database / ID | EM DATA BANK (EMDB) / 1499 |
|---|---|
| Title | Structure of the E. coli trigger factor bound to a translating ribosome |
| Map | Structure of the E. coli trigger factor bound to a translating ribosome |
| Sample | Escherichia coli Trigger Factor associated with an Escherichia coli ribosome-nascent chain complex |
| Keywords |  trigger factor, ribosome-nascent chain complex, translating ribosome, co-translational protein folding, chaperone |
| Authors | Merz F, Boehringer D, Schaffitzel C, Preissler S, Hoffmann A, Maier T, Rutkowska A, Lozza J, Ban N, Bukau B, Deuerling E |
| Date | Deposition: 2008-04-04, Header release: 2008-04-04, Map release: 2009-05-29, Last update: 2013-03-13 |
| EMDB Sites |  EMDB @PDBe (EU), EMDB @RCSB (USA) |
| Structure Visualization | |
| Movies |  Movie Page#1: Surface view with section colored by density value, Surface level: 200, Made by UCSF CHIMERA #2: Surface view colored by height, Surface level: 200, Made by UCSF CHIMERA #3: Surface view with fitted model, atomic models: PDB-2vrh, Surface level: 200, Made by UCSF CHIMERA #4: Simplified surface model with fitted atomic model: PDB-2vrh, Made by Jmol |
| Supplemental images | |
| Structure viewers |  Yorodumi,  Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe) |
| Related Structure Data | |
| Related Entries |
Cite: data citing same article Fit: output model of fitting |
| Similar strucutres (beta) |
 List of similar structure data  about Omokage system |
 Article | |
| Citation - Primary | |
| Article | EMBO J., Vol. 27, Issue 11, Page 1622-32, 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 Zentrum für Molekulare Biologie Heidelberg, DKFZ-ZMBH Alliance, Universität Heidelberg, Heidelberg, Germany. |
| Keywords | Amino Acid Sequence, Cross-Linking Reagents (chemistry), Cryoelectron Microscopy, Escherichia coli Proteins (chemistry), Molecular Chaperones (chemistry), Peptides (chemistry), Peptidylprolyl Isomerase (chemistry, 5.2.1.8), Protein Biosynthesis, Protein Conformation, Protein Folding, Protein Structure, Tertiary, Ribosomes (chemistry), trigger factor, E coli (5.2.1.-) |
| Links | DOI: 10.1038/emboj.2008.89, PubMed: 18497744, PMC: PMC2426727 |
 Map | |||||||||||||||||||||||||
| File |  EMD-1499.map ( map file in CCP4 format, 3540 KB ) | ||||||||||||||||||||||||
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| Projections & Slices | Size of images:
Images are generated by Spider package. | ||||||||||||||||||||||||
| Density |
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| Data Type | Image stored as Reals | ||||||||||||||||||||||||
| Space Group Number | 1 | ||||||||||||||||||||||||
| Map Geometry |
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| Unit Cell | A= B= C: 406.4 A Alpha=beta=gamma: 90 degrees | ||||||||||||||||||||||||
| Pixel Spacing | X= Y= Z: 4.23333 A | ||||||||||||||||||||||||
| CCP4 map header info | |||||||||||||||||||||||||
| Annotation Details | Structure of the E. coli trigger factor bound to a translating ribosome | ||||||||||||||||||||||||
 Supplement | |
| Images | |
| Images | |
|---|---|
 Sample | |
| Name | Escherichia coli Trigger Factor associated with an Escherichia coli ribosome-nascent chain complex |
|---|---|
| Number of Components | 2 |
| Details | monodisperse sample |
| Experimental Mass | 2.6MDa |
| Component #1: ribosome-prokaryote - translating ribosome | |
| Scientific name | ribosome-nascent chain complex |
| Common Name | translating ribosome |
| Details | SecM-stalled E. coli ribosome complex |
| Scientific Name of Species | Escherichia coli
|
| NCBI taxonomy | 562 |
| Prokaryote | ALL |
| Recombinant expression | No |
| Component #2: protein - trigger factor | |
| Scientific name | trigger factor |
| Details | trigger factor crosslinked to the nascent chain. Mutant TFS61C E. coli |
| Oligomeric Details | monomer |
| Scientific Name of Species | Escherichia coli |
| NCBI taxonomy | 562 |
| Strain | mutant TFS61c |
| Recombinant expression | No |
 Experiment | |
| Sample Preparation | |
| Specimen State | particle |
|---|---|
| Buffer | Details: 50 mM Hepes-KOH pH 7.5, 100 mM KCl, 25 mM MgCl2, 0.5 mg/ml chloramphenicol pH: 7.5 |
| Vitrification | |
| Cryogen Name | ETHANE |
| Instrument | NONE |
| Imaging | |
| Microscope | FEI TECNAI F20 |
| Electron Gun | |
| Electron Source | FIELD EMISSION GUN |
| Accelerating Voltage | 200 kV |
| Illumination Mode | FLOOD BEAM |
| Lens | |
| Magnification | Nominal: 50000, Calibrated: 50000 |
| Imaging Mode | BRIGHT FIELD |
| Defocus | 1500 nm - 3500 nm |
| Specimen Holder | |
| Holder | Side entry liquid nitrogen-cooled cryo specimen holder |
| Model | GATAN LIQUID NITROGEN |
| Temperature | 88 K |
| Camera | |
| Detector | Kodak SO163 film |
| Image Acquisition | |
| Scanner | OTHER |
| Sampling Size | 6.35 |
| Details | rotating-drum scanner |
 Processing | |
| Method | single particle reconstruction |
|---|---|
| 3D reconstruction | |
| Algorithm | angular reconstitution |
| Software | IMAGIC-5, SPIDER |
| CTF Correction | each image |
| Details | Final rounds of refinement were done using the Spider software |
| Resolution By Author | 19 A |
| Resolution Method | FSC at 0.5 cut-off |
| Atomic Model Fitting | |
| Model #0 | |
| Details | Protocol: Rigid Body. exhaustive search |
| Refinement Protocol | rigid body |
| Refinement Space | REAL |
| Target Criteria | Cross Correlation |
| PDB Entry ID | 1W26 |
| PDB Chain ID | A |
| Model #1 | |
| Refinement Space | REAL |
| Refinement Protocol | rigid body |
| Details | Protocol: Rigid Body |
| Software | MOLREP |
| PDB Entry ID | 2AW4 |
| Fitted Coordinate | |
| PDB entry ID | |
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