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- EMDB-4118: CryoEM structure of the membrane pore complex of Pneumolysin at 4.5A -

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Basic information

Entry
Database: EMDB / ID: 4118
TitleCryoEM structure of the membrane pore complex of Pneumolysin at 4.5A
Map dataPLY pore complex
SamplePneumolysin pore complex:
Pneumolysin
Function / homologyThiol-activated cytolysin / Thiol-activated cytolysin C-terminal / Thiol-activated cytolysin superfamily / Thiol-activated cytolysin, alpha-beta domain superfamily / Thiol-activated cytolysin, C-terminal domain superfamily / Thiol-activated cytolysin / Thiol-activated cytolysin beta sandwich domain / Thiol-activated cytolysins signature. / cholesterol binding / hemolysis in other organism ...Thiol-activated cytolysin / Thiol-activated cytolysin C-terminal / Thiol-activated cytolysin superfamily / Thiol-activated cytolysin, alpha-beta domain superfamily / Thiol-activated cytolysin, C-terminal domain superfamily / Thiol-activated cytolysin / Thiol-activated cytolysin beta sandwich domain / Thiol-activated cytolysins signature. / cholesterol binding / hemolysis in other organism / toxin activity / host cell plasma membrane / integral component of membrane / extracellular region / Pneumolysin
Function and homology information
SourceStreptococcus pneumoniae (bacteria)
Methodsingle particle reconstruction / cryo EM / 4.5 Å resolution
Authorsvan Pee K / Neuhaus A
CitationJournal: 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
Validation ReportPDB-ID: 5ly6

SummaryFull reportAbout validation report
DateDeposition: Sep 24, 2016 / Header (metadata) release: Oct 26, 2016 / Map release: Apr 5, 2017 / Last update: Aug 2, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-5ly6
  • Surface level: 0.022
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-5ly6
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4118.png

Downloads & links

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Map

Fileemd_4118.map.gz (map file in CCP4 format, 186625 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
360 pix
1.4 Å/pix.
= 504. Å		360 pix
1.4 Å/pix.
= 504. Å		360 pix
1.4 Å/pix.
= 504. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4 Å
Density

Histogram

Histogram (log scale)
Contour Level:0.0282 (by author), 0.02 (movie #1):
Minimum - Maximum-0.022703713 - 0.079944775
Average (Standard dev.)0.0008561607 (0.0045818426)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions360360360
Origin000
Limit359359359
Spacing360360360
CellA=B=C: 504 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.41.41.4
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z504.000504.000504.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.0230.0800.001

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Supplemental data

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Sample components

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Entire Pneumolysin pore complex

EntireName: Pneumolysin pore complex / Number of components: 2
MassTheoretical: 2.2 MDa

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Component #1: cellular-component, Pneumolysin pore complex

Cellular-componentName: Pneumolysin pore complex / Recombinant expression: No
MassTheoretical: 2.2 MDa
SourceSpecies: Streptococcus pneumoniae (bacteria)
Source (engineered)Expression System: Escherichia coli BL21 (bacteria) / Vector: pET15

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Component #2: protein, Pneumolysin

ProteinName: Pneumolysin / Recombinant expression: No
MassTheoretical: 52.866066 kDa
Source (engineered)Expression System: Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466) (bacteria)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 1 mg/ml / pH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.02 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C42 (42 fold cyclic) / Number of projections: 6461
3D reconstructionSoftware: RELION / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Modeling #1Refinement protocol: flexible
Input PDB model: 5AOD

5aod


Chain ID: 5AOD_A
Output model

5ly6

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