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- PDB-5ly6: CryoEM structure of the membrane pore complex of Pneumolysin at 4.5A -

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Entry
Database: PDB / ID: 5ly6
TitleCryoEM structure of the membrane pore complex of Pneumolysin at 4.5A
DescriptorPneumolysin
KeywordsTOXIN / Bacterial toxins / pore complex / cryoEM structure / cholesterol-dependent cytolysin / Pneumolysin / membrane pore
Specimen sourceStreptococcus pneumoniae serotype 2 (strain d39 / nctc 7466) / bacteria
MethodElectron microscopy (4.5 A resolution / Single particle)
Authorsvan Pee, K. / Neuhaus, A. / D'Imprima, E. / Mills, D.J. / Kuehlbrandt, W. / Yildiz, O.
CitationElife, 2017, 6

Elife, 2017, 6 StrPapers
CryoEM structures of membrane pore and prepore complex reveal cytolytic mechanism of Pneumolysin.
Katharina van Pee / Alexander Neuhaus / Edoardo D'Imprima / Deryck J Mills / Werner Kühlbrandt / Özkan Yildiz

DateDeposition: Sep 24, 2016 / Release: Apr 5, 2017

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Assembly

Deposited unit
B: Pneumolysin


Theoretical massNumber of molelcules
Total (without water)52,8661
Polyers52,8661
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (A2)0
ΔGint (kcal/M)0
Surface area (A2)29420
MethodPISA

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Components

#1: Polypeptide(L)Pneumolysin / Thiol-activated cytolysin


Mass: 52866.066 Da / Num. of mol.: 1
Source: (gene. exp.) Streptococcus pneumoniae serotype 2 (strain d39 / nctc 7466) / bacteria
References: UniProt: Q04IN8

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentReconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: Pneumolysin pore complex / Type: ORGANELLE OR CELLULAR COMPONENT
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyMicroscope model: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD

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Processing

3D reconstructionResolution: 4.5 A / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 6461
Atomic model buildingRef protocol: AB INITIO MODEL
Atomic model buildingPDB-ID: 5AOD
Pdb chain id: A

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