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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: EMD-4118
TitleCryoEM structure of the membrane pore complex of Pneumolysin at 4.5A
Map dataPLY pore complex
Sample
  • Organelle or cellular component: Pneumolysin pore complex
    • Protein or peptide: Pneumolysin
KeywordsBacterial toxins / pore complex / cryoEM structure / cholesterol-dependent cytolysin / Pneumolysin / membrane pore / TOXIN
Function / homology
Function and homology information


cholesterol binding / toxin activity / killing of cells of another organism / host cell plasma membrane / extracellular region / membrane
Similarity search - Function
Thiol-activated cytolysins signature. / Thiol-activated cytolysin C-terminal / Thiol-activated cytolysin, C-terminal domain superfamily / Thiol-activated cytolysin beta sandwich domain / Thiol-activated cytolysin / Thiol-activated cytolysin superfamily / Thiol-activated cytolysin, alpha-beta domain superfamily / Thiol-activated cytolysin
Similarity search - Domain/homology
Biological speciesStreptococcus pneumoniae (bacteria) / Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
Authorsvan Pee K / Neuhaus A
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck SocietyBiophysics/Structural Biology Germany
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 /
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.
History
DepositionSep 24, 2016-
Header (metadata) releaseOct 26, 2016-
Map releaseApr 5, 2017-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • 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
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-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

FileDownload / File: emd_4118.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPLY pore complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.4 Å/pix.
x 360 pix.
= 504. Å		1.4 Å/pix.
x 360 pix.
= 504. Å		1.4 Å/pix.
x 360 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 LevelBy AUTHOR: 0.0282 / Movie #1: 0.02
Minimum - Maximum-0.022703713 - 0.079944775
Average (Standard dev.)0.0008561607 (±0.0045818426)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 504.0 Å
α=β=γ: 90.0 °

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
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
Components
  • Organelle or cellular component: Pneumolysin pore complex
    • Protein or peptide: Pneumolysin

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Supramolecule #1: Pneumolysin pore complex

SupramoleculeName: Pneumolysin pore complex / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Streptococcus pneumoniae (bacteria)
Molecular weightTheoretical: 2.2 MDa

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Macromolecule #1: Pneumolysin

MacromoleculeName: Pneumolysin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466) (bacteria)
Molecular weightTheoretical: 52.866066 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MANKAVNDFI LAMNYDKKKL LTHQGESIEN RFIKEGNQLP DEFVVIERKK RSLSTNTSDI SVTATNDSRL YPGALLVVDE TLLENNPTL LAVDRAPMTY SIDLPGLASS DSFLQVEDPS NSSVRGAVND LLAKWHQDYG QVNNVPARMQ YEKITAHSME Q LKVKFGSD ...String:
MANKAVNDFI LAMNYDKKKL LTHQGESIEN RFIKEGNQLP DEFVVIERKK RSLSTNTSDI SVTATNDSRL YPGALLVVDE TLLENNPTL LAVDRAPMTY SIDLPGLASS DSFLQVEDPS NSSVRGAVND LLAKWHQDYG QVNNVPARMQ YEKITAHSME Q LKVKFGSD FEKAANSLDI DFNAVHSGEK QIQIVNFKQI YYTVSVDAVK NPGDVFQDTV TVEDLKQRGI SAERPLVYIS SV AYGRQVY LKLETTSKSD EVQAAFEAAI LGVKVAPQTQ WKQILDNTEV KAVILGGDPS SGARVVTGKV DMVEDLIQEG SRF TADHPG LPISYTTSFL RDNVVATFQN STDYVETKVT AYRNGDLLLD HSGAYVAQYY ITWDELSYDH QGKEVLTPKA WDRN GQDLT AHFTTSIPLK GNVRNLSVKI RECTGLAWEW WRTVYEKTDL PLVRKRTISI WGTTLYPQVE DKVEND

UniProtKB: Pneumolysin

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average exposure time: 6.0 sec. / Average electron dose: 1.02 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

2983

Final reconstructionApplied symmetry - Point group: C42 (42 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 6461
Initial angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 1.4)
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 1.4)
Final 3D classificationNumber classes: 2 / Software - Name: RELION (ver. 1.4)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5aod


Chain - Chain ID: A / Chain - Residue range: 1-471 / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: AB INITIO MODEL
Output model

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

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