|Entry||Database: EMDB / ID: 8855|
|Title||Cryo-EM structure of P. aeruginosa flagellar filaments A443V|
|Sample||Pseudomonas aeruginosa flagella filament|
|Source||Pseudomonas aeruginosa pao1 / bacteria|
|Map data||Cryo-EM structure of P. aeruginosa flagellar filaments A443V|
|Method||helical reconstruction, at 4.2 Å resolution|
|Authors||Wang F / Postel S|
|Citation||Nat Commun, 2017, 8, 960-960|
|Validation Report||PDB-ID: 5wk5|
SummaryFull reportAbout validation report
|Date||Deposition: Jul 24, 2017 / Header (metadata) release: Aug 30, 2017 / Map release: Oct 25, 2017 / Last update: Nov 1, 2017|
Downloads & links
|File||emd_8855.map.gz (map file in CCP4 format, 193601 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 1.05 Å|
CCP4 map header:
-Entire Pseudomonas aeruginosa flagella filament
|Entire||Name: Pseudomonas aeruginosa flagella filament / Number of components: 2|
-Component #1: protein, Pseudomonas aeruginosa flagella filament
|Protein||Name: Pseudomonas aeruginosa flagella filament / Recombinant expression: No|
|Source||Species: Pseudomonas aeruginosa pao1 / bacteria|
|Source (engineered)||Expression System: Pseudomonas aeruginosa pao1 / bacteria|
-Component #2: protein, B-type flagellin
|Protein||Name: B-type flagellin / Recombinant expression: No|
|Mass||Theoretical: 49.302906 kDa|
|Source (engineered)||Expression System: Pseudomonas aeruginosa (strain atcc 15692 / dsm 22644 / cip 104116 / jcm 14847 / lmg 12228 / 1c / prs 101 / pao1) / bacteria|
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
|Helical parameters||Axial symmetry: C1 (asymmetric) / Delta z: 4.61 Å / Delta phi: 65.75 deg.|
|Sample solution||Specimen conc.: 0.1 mg/ml / Buffer solution: PBS / pH: 7.4|
|Vitrification||Cryogen name: ETHANE / Humidity: 90 %|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 20 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Imaging mode: BRIGHT FIELD|
|Specimen Holder||Model: OTHER|
|Camera||Detector: FEI FALCON II (4k x 4k)|
|Image acquisition||Details: Images were stored containing seven parts, where each part represented a set of frames corresponding to a dose of ~20 electrons per Angstrom^2. The full dose image stack was used for the estimation of the CTF as well as for boxing filaments. Only the first two parts were used for the reconstruction (~5 electrons per Angstrom^2).|
|Processing||Method: helical reconstruction|
|3D reconstruction||Algorithm: BACK PROJECTION / Software: SPIDER / Resolution: 4.2 Å / Resolution method: OTHER / Details: model-map FSC 0.38 cut-off|
-Atomic model buiding
-Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017
Three pioneers of this field were awarded Nobel Prize in Chemistry 2017
- Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
- Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
- Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.
External links: The 2017 Nobel Prize in Chemistry - Press Release
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