|Entry||Database: EMDB / ID: 8608|
|Title||Structure of E. coli MCE protein PqiB, periplasmic domain|
|Sample||homo hexamer of PqiB|
|Source||Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /|
|Map data||E. coli MCE protein PqiB, periplasmic domain|
|Method||single particle reconstruction, at 3.96 Å resolution|
|Authors||Bhabha G / Ekiert DC|
|Citation||Cell, 2017, 169, 273-285.e17|
|Validation Report||PDB-ID: 5uvn|
SummaryFull reportAbout validation report
|Date||Deposition: Feb 20, 2017 / Header (metadata) release: Apr 12, 2017 / Map release: Apr 12, 2017 / Last update: Sep 27, 2017|
Downloads & links
|File||emd_8608.map.gz (map file in CCP4 format, 32001 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 1.31 Å|
CCP4 map header:
-Entire homo hexamer of PqiB
|Entire||Name: homo hexamer of PqiB / Number of components: 2|
|Mass||Theoretical: 347 kDa|
-Component #1: protein, homo hexamer of PqiB
|Protein||Name: homo hexamer of PqiB / Recombinant expression: No|
|Mass||Theoretical: 347 kDa|
|Source||Species: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 / |
|Source (engineered)||Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /|
-Component #2: protein, Paraquat-inducible protein B
|Protein||Name: Paraquat-inducible protein B / Recombinant expression: No|
|Mass||Theoretical: 48.857043 kDa|
|Source (engineered)||Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 / |
|Sample solution||Buffer solution: 20 mM Tris pH 8.0 and 150 mM NaCl / pH: 8|
|Vitrification||Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE|
-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: 80 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Imaging mode: BRIGHT FIELD|
|Specimen Holder||Model: OTHER|
|Camera||Detector: GATAN K2 (4k x 4k)|
|Image acquisition||Details: 80 e/A2 is total dose for 50 frames|
|Processing||Method: single particle reconstruction / Applied symmetry: C6 (6 fold cyclic) / Number of projections: 36591|
|3D reconstruction||Software: RELION / Resolution: 3.96 Å / Resolution method: FSC 0.143 CUT-OFF|
|FSC plot (resolution assessment)|
-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
-Jul 12, 2017. Major update of PDB
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