|Entry||Database: EMDB / ID: 1499|
|Title||Structure of the E. coli trigger factor bound to a translating ribosome|
|Keywords||trigger factor / ribosome-nascent chain complex / translating ribosome / co-translational protein folding / chaperone|
|Sample||Escherichia coli Trigger Factor associated with an Escherichia coli ribosome-nascent chain complex|
|Source||Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /|
|Map data||Structure of the E. coli trigger factor bound to a translating ribosome|
|Method||single particle reconstruction, at 19 Å resolution|
|Authors||Merz F / Boehringer D / Schaffitzel C / Preissler S / Hoffmann A / Maier T / Rutkowska A / Lozza J / Ban N / Bukau B / Deuerling E|
|Citation||EMBO J., 2008, 27, 1622-1632|
EMBO J., 2008, 27, 1622-1632 Yorodumi Papers
|Validation Report||PDB-ID: 2vrh|
SummaryFull reportAbout validation report
|Date||Deposition: Apr 4, 2008 / Header (metadata) release: Apr 4, 2008 / Map release: May 29, 2009 / Last update: Mar 13, 2013|
Downloads & links
|File||emd_1499.map.gz (map file in CCP4 format, 3457 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 4.23333 Å|
CCP4 map header:
-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|
Details: monodisperse sample / Number of components: 2
|Mass||Experimental: 2.6 MDa|
-Component #1: ribosome-prokaryote, ribosome-nascent chain complex
|Ribosome-prokaryote||Name: ribosome-nascent chain complex / a.k.a: translating ribosome / Details: SecM-stalled E. coli ribosome complex / Prokaryote: ALL / Recombinant expression: No|
|Source||Species: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /|
-Component #2: protein, trigger factor
|Protein||Name: trigger factor / a.k.a: trigger factor / Oligomeric Details: monomer|
Details: trigger factor crosslinked to the nascent chain. Mutant TFS61C E. coli
Recombinant expression: No
|Source||Species: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 / |
Strain: mutant TFS61c
|Sample solution||Buffer solution: 50 mM Hepes-KOH pH 7.5, 100 mM KCl, 25 mM MgCl2, 0.5 mg/ml chloramphenicol|
|Vitrification||Instrument: NONE / Cryogen name: ETHANE|
-Electron microscopy imaging
Model: Tecnai F20 / Image courtesy: FEI Company
|Imaging||Microscope: FEI TECNAI F20|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 50000 X (nominal), 50000 X (calibrated) / Imaging mode: BRIGHT FIELD / Defocus: 1500 - 3500 nm|
|Specimen Holder||Holder: Side entry liquid nitrogen-cooled cryo specimen holder|
Model: GATAN LIQUID NITROGEN / Temperature: 88 K
|Camera||Detector: KODAK SO-163 FILM|
|Image acquisition||Scanner: OTHER / Sampling size: 6.35 microns / Details: rotating-drum scanner|
|Processing||Method: single particle reconstruction / Applied symmetry: C1 (asymmetric)|
|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: 19 Å / Resolution method: FSC 0.5
-Atomic model buiding
|Modeling #1||Refinement protocol: rigid body / Target criteria: Cross Correlation / Refinement space: REAL / Details: Protocol: Rigid Body. exhaustive search|
Input PDB model: 1W26
Chain ID: A
|Modeling #2||Software: MOLREP / Refinement protocol: rigid body / Refinement space: REAL / Details: Protocol: Rigid Body|
Input PDB model: 2AW4
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External links: The 2017 Nobel Prize in Chemistry - Press Release
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