|Entry||Database: PDB / ID: 5ly6|
|Title||CryoEM structure of the membrane pore complex of Pneumolysin at 4.5A|
|Keywords||TOXIN / Bacterial toxins / pore complex / cryoEM structure / cholesterol-dependent cytolysin / Pneumolysin / membrane pore|
|Specimen source||Streptococcus pneumoniae serotype 2 (strain d39 / nctc 7466) / bacteria|
|Method||Electron microscopy (4.5 Å resolution / Particle / Single particle)|
|Authors||van Pee, K. / Neuhaus, A. / D'Imprima, E. / Mills, D.J. / Kuehlbrandt, W. / Yildiz, O.|
|Citation||Elife, 2017, 6|
SummaryFull reportAbout validation report
|Date||Deposition: Sep 24, 2016 / Release: Apr 5, 2017|
Downloads & links
Mass: 52866.066 Da / Num. of mol.: 1
Source: (gene. exp.) Streptococcus pneumoniae serotype 2 (strain d39 / nctc 7466) / bacteria
References: UniProt: Q04IN8
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE|
|Component||Name: Pneumolysin pore complex / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: 1 / Source: RECOMBINANT|
|Molecular weight||Value: 2.2 deg. / Units: MEGADALTONS|
|Source (natural)||Organism: Streptococcus pneumoniae|
|Source (recombinant)||Organism: Escherichia coli BL21 / Plasmid: pET15|
|Buffer solution||pH: 7|
|Specimen||Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES|
|Vitrification||Cryogen name: ETHANE|
-Electron microscopy imaging
Model: Tecnai Polara / Image courtesy: FEI Company
|Microscopy||Microscope model: FEI POLARA 300|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM|
|Electron lens||Mode: BRIGHT FIELD|
|Image recording||Average exposure time: 6 sec. / Electron dose: 1.02 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)|
|CTF correction||Type: PHASE FLIPPING AND AMPLITUDE CORRECTION|
|Symmetry||Point symmetry: C42|
|3D reconstruction||Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 6461 / Symmetry type: POINT|
|Atomic model building||Ref protocol: AB INITIO MODEL|
|Atomic model building||PDB-ID: 5AOD|
Pdb chain ID: A / Pdb chain residue range: 1-471
-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.
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- 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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