|Entry||Database: EMDB / ID: 3918|
|Title||Recombinant human Bri2 BRICHOS domain, oligomeric state|
|Sample||Oligomeric Bri2 BRICHOS|
|Source||Homo sapiens / human|
|Map data||Negative stain 3D density map of the Bri2 Brichos domain in its oligomeric state, Molecular wieght, 370 kDaMethod: Single particle TEM|
|Method||single particle reconstruction, at 16.5 Å resolution|
|Authors||Hebert H / Johansson J / Nilsson HE / Koeck PJB / Chen G|
|Citation||Nat Commun, 2017, 8, 2081-2081|
Nat Commun, 2017, 8, 2081-2081 Yorodumi Papers
|Date||Deposition: Oct 12, 2017 / Header (metadata) release: Dec 20, 2017 / Map release: Dec 27, 2017 / Last update: Dec 27, 2017|
Downloads & links
|File||emd_3918.map.gz (map file in CCP4 format, 4500 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 2.076 Å|
CCP4 map header:
-Entire Oligomeric Bri2 BRICHOS
|Entire||Name: Oligomeric Bri2 BRICHOS / Number of components: 2|
|Mass||Experimental: 370 kDa|
-Component #1: cellular-component, Oligomeric Bri2 BRICHOS
|Cellular-component||Name: Oligomeric Bri2 BRICHOS / Recombinant expression: No|
|Mass||Experimental: 370 kDa|
|Source||Species: Homo sapiens / human|
|Source (engineered)||Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 / |
Vector: pET / Strain: Shuttle T7
-Component #2: protein, Bri2 BRICHOS domain
|Protein||Name: Bri2 BRICHOS domain / Recombinant expression: No|
|Source (engineered)||Expression System: Homo sapiens / human / Strain: Human|
|Sample solution||Specimen conc.: 0.047 mg/ml / pH: 8|
|Staining||2% Uranyl Acetate|
|Vitrification||Cryogen name: NONE|
-Electron microscopy imaging
|Imaging||Microscope: JEOL 2100F / Details: per frame =1.44 e/A2|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 57.5 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 60000 X (nominal), 61680 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD|
|Specimen Holder||Model: JEOL|
|Image acquisition||Number of digital images: 24|
Details: Negative stain images were collected in movie-mode at 20 frames per second. For each exposure, the comprised frames were drift corrected using the DE_process_frames-2.7.1.py script
|Processing||Method: single particle reconstruction / Applied symmetry: D2 (2*2 fold dihedral) / Number of projections: 2718|
|3D reconstruction||Algorithm: FOURIER SPACE / Software: EMAN2|
CTF correction: For low resolution data EMAN2 use a 1D structure factor during the CTF procedure
Resolution: 16.5 Å / Resolution method: FSC 0.143 CUT-OFF
-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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