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

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Basic information

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 Å resolution / Particle / 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

Validation Report
SummaryFull reportAbout validation report
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 (Å2)0
ΔGint (kcal/M)0
Surface area (Å2)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

Cellular component

Molecular function

Biological process

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: Pneumolysin pore complex / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: 1 / Source: RECOMBINANT
Molecular weightValue: 2.2 deg. / Units: MEGADALTONS
Source (natural)Organism: Streptococcus pneumoniae
Source (recombinant)Organism: Escherichia coli BL21 / Plasmid: pET15
Buffer solutionpH: 7
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingAverage exposure time: 6 sec. / Electron dose: 1.02 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategoryImage processing IDImaging IDFitting ID
1Relion1.4PARTICLE SELECTION1
2Relion1.4IMAGE ACQUISITION1
4CTFFIND3CTF CORRECTION1
7coot8.4MODEL FITTING1
9relion1.4INITIAL EULER ASSIGNMENT1
10relion1.4FINAL EULER ASSIGNMENT1
11relion1.4CLASSIFICATION1
12relion1.4RECONSTRUCTION1
13coot8.4MODEL REFINEMENT1
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C42
3D reconstructionResolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 6461 / Symmetry type: POINT
Atomic model buildingRef protocol: AB INITIO MODEL
Atomic model buildingPDB-ID: 5AOD
Pdb chain ID: A / Pdb chain residue range: 1-471

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