|Entry||Database: EMDB / ID: 4118|
|Title||CryoEM structure of the membrane pore complex of Pneumolysin at 4.5A|
|Map data||PLY pore complex|
|Sample||Pneumolysin pore complex|
|Function/homology||Thiol-activated cytolysins signature. / Thiol-activated cytolysin / Thiol-activated cytolysin C-terminal / Thiol-activated cytolysin superfamily / Thiol-activated cytolysin, alpha-beta domain superfamily / Thiol-activated cytolysin / Thiol-activated cytolysin beta sandwich domain / cholesterol binding / hemolysis in other organism / toxin activity ...Thiol-activated cytolysins signature. / Thiol-activated cytolysin / Thiol-activated cytolysin C-terminal / Thiol-activated cytolysin superfamily / Thiol-activated cytolysin, alpha-beta domain superfamily / Thiol-activated cytolysin / Thiol-activated cytolysin beta sandwich domain / cholesterol binding / hemolysis in other organism / toxin activity / host cell plasma membrane / integral component of membrane / extracellular region / Pneumolysin|
Function and homology information
|Source||Streptococcus pneumoniae / / bacteria|
|Method||Cryo EM / single particle reconstruction / 4.5 Å resolution|
|Authors||van Pee K / Neuhaus A|
|Citation||Journal: Elife / Year: 2017|
Title: CryoEM structures of membrane pore and prepore complex reveal cytolytic mechanism of Pneumolysin.
Authors: Katharina van Pee / Alexander Neuhaus / Edoardo D'Imprima / Deryck J Mills / Werner Kühlbrandt / Özkan Yildiz
Abstract: Many pathogenic bacteria produce pore-forming toxins to attack and kill human cells. We have determined the 4.5 Å structure of the ~2.2 MDa pore complex of pneumolysin, the main virulence factor of ...Many pathogenic bacteria produce pore-forming toxins to attack and kill human cells. We have determined the 4.5 Å structure of the ~2.2 MDa pore complex of pneumolysin, the main virulence factor of , by cryoEM. The pneumolysin pore is a 400 Å ring of 42 membrane-inserted monomers. Domain 3 of the soluble toxin refolds into two ~85 Å β-hairpins that traverse the lipid bilayer and assemble into a 168-strand β-barrel. The pore complex is stabilized by salt bridges between β-hairpins of adjacent subunits and an internal α-barrel. The apolar outer barrel surface with large sidechains is immersed in the lipid bilayer, while the inner barrel surface is highly charged. Comparison of the cryoEM pore complex to the prepore structure obtained by electron cryo-tomography and the x-ray structure of the soluble form reveals the detailed mechanisms by which the toxin monomers insert into the lipid bilayer to perforate the target membrane.
|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|
|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|
|Specimen||Specimen state: particle / Method: Cryo EM|
|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)|
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