|Entry||Database: EMDB / ID: 5741|
|Title||Single-particle Electron Microscopy Structure of the TRAPPIII Complex|
|Sample||Recombinant TRAPPIII complex|
|Source||Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /|
|Map data||Reconstruction of yeast TRAPPIII complex, filtered to 22 Angstrom resolution|
|Method||single particle reconstruction, at 22 Å resolution|
|Authors||Tan D / Cai Y / Wang J / Zhang J / Menon S / Chou H-T / Ferro-Novick S / Reinisch KM / Walz T|
|Citation||Proc. Natl. Acad. Sci. U.S.A., 2013, 110, 19432-19437|
Proc. Natl. Acad. Sci. U.S.A., 2013, 110, 19432-19437 Yorodumi Papers
|Date||Deposition: Aug 12, 2013 / Header (metadata) release: Sep 4, 2013 / Map release: Nov 13, 2013 / Last update: Dec 11, 2013|
Downloads & links
|File||emd_5741.map.gz (map file in CCP4 format, 2001 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 4.48 Å|
CCP4 map header:
-Entire Recombinant TRAPPIII complex
|Entire||Name: Recombinant TRAPPIII complex / Number of components: 1 / Oligomeric State: oligomer|
|Mass||Theoretical: 254 kDa / Experimental: 254 kDa|
-Component #1: protein, transport protein particle III
|Protein||Name: transport protein particle III / Oligomeric Details: monomer / Recombinant expression: Yes / Number of Copies: 1|
|Mass||Theoretical: 254 kDa / Experimental: 254 kDa|
|Source||Species: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /|
|Source (engineered)||Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 / |
Vector: pETDuet / Strain: BL21
|Sample solution||Specimen conc.: 0.4 mg/ml / Buffer solution: 20mM Tris-HCl, 300 mM NaCl, 1mM DTT / pH: 8|
|Support film||200 mesh copper grids with thin carbon support, glow discharged|
|Staining||Grids with adsorbed protein stained with 0.75% uranyl format for 20 seconds|
|Vitrification||Instrument: NONE / Cryogen name: NONE|
-Electron microscopy imaging
|Imaging||Microscope: FEI TECNAI 12 / Date: Dec 20, 2010 / Details: low dose setting|
|Electron gun||Electron source: LAB6 / Accelerating voltage: 120 kV / Electron dose: 10 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 67000 X (nominal), 67000 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 1500 nm|
|Specimen Holder||Model: SIDE ENTRY, EUCENTRIC / Tilt Angle: 0 - 60 deg.|
|Camera||Detector: GENERIC IMAGE PLATES|
|Image acquisition||Number of digital images: 133 / Scanner: OTHER / Sampling size: 15 microns|
|Processing||Method: single particle reconstruction / Number of class averages: 20 / Applied symmetry: C1 (asymmetric) / Number of projections: 1120|
Details: Random Conical Tilt reconstruction using Spider scripts
|3D reconstruction||Algorithm: random conical tilt / Software: Spider|
Details: Final maps were calculated from a dataset of two class-averages
Resolution: 22 Å / Resolution method: FSC 0.5
-Atomic model buiding
|Modeling #1||Software: Chimera / Refinement protocol: flexible / Refinement space: REAL|
Input PDB model: 2J3T
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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.
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External links: The 2017 Nobel Prize in Chemistry - Press Release
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