|Entry||Database: EMDB / ID: 4118|
|Title||CryoEM structure of the membrane pore complex of Pneumolysin at 4.5A|
|Sample||Pneumolysin pore complex|
|Source||Streptococcus pneumoniae / bacteria / ストレプトコッカス・ニューモニアエ, 肺炎レンサ球菌|
|Map data||PLY pore complex|
|Method||single particle reconstruction, at 4.5 Å resolution|
|Authors||van Pee K / Neuhaus A|
|Citation||Elife, 2017, 6|
|Validation Report||PDB-ID: 5ly6|
SummaryFull reportAbout validation report
|Date||Deposition: Sep 24, 2016 / Header (metadata) release: Oct 26, 2016 / Map release: Apr 5, 2017 / Last update: Aug 2, 2017|
Downloads & links
|File||emd_4118.map.gz (map file in CCP4 format, 186625 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 1.4 Å|
CCP4 map header:
-Entire Pneumolysin pore complex
|Entire||Name: Pneumolysin pore complex / Number of components: 2|
|Mass||Theoretical: 2.2 MDa|
-Component #1: cellular-component, Pneumolysin pore complex
|Cellular-component||Name: Pneumolysin pore complex / Recombinant expression: No|
|Mass||Theoretical: 2.2 MDa|
|Source||Species: Streptococcus pneumoniae / bacteria / ストレプトコッカス・ニューモニアエ, 肺炎レンサ球菌|
|Source (engineered)||Expression System: Escherichia coli bl21 / bacteria / image: Escherichia coli|
-Component #2: protein, Pneumolysin
|Protein||Name: Pneumolysin / Recombinant expression: No|
|Mass||Theoretical: 52.866066 kDa|
|Source (engineered)||Expression System: Streptococcus pneumoniae serotype 2 (strain d39 / nctc 7466) / bacteria|
|Sample solution||Specimen conc.: 1 mg/ml / pH: 7|
|Vitrification||Cryogen name: ETHANE|
-Electron microscopy imaging
Model: Tecnai Polara / Image courtesy: FEI Company
|Imaging||Microscope: FEI POLARA 300|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.02 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Imaging mode: BRIGHT FIELD|
|Specimen Holder||Model: OTHER|
|Camera||Detector: GATAN K2 (4k x 4k)|
|Processing||Method: single particle reconstruction / Applied symmetry: C42 (42 fold cyclic) / Number of projections: 6461|
|3D reconstruction||Software: RELION / Resolution: 4.5 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
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