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- EMDB-9212: 12-meric ClyA pore complex -

Open data

ID or keywords:


Basic information

Database: EMDB / ID: EMD-9212
Title12-meric ClyA pore complex
Map data
Sample12-meric ClyA pore complex:
Hemolysin E, chromosomal
Function / homology
Function and homology information

modulation of apoptotic process in other organism / cytolysis by symbiont of host cells / hemolysis in other organism / toxin activity / periplasmic space / pathogenesis / host cell plasma membrane / integral component of membrane / extracellular region / identical protein binding
Hemolysin E
Hemolysin E, chromosomal
Biological speciesEscherichia coli (E. coli) / Escherichia coli (strain K12) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsPeng W / de Souza Santos M / Li Y / Tomchick DR / Orth K
CitationJournal: PLoS ONE / Year: 2019
Title: High-resolution cryo-EM structures of the E. coli hemolysin ClyA oligomers.
Authors: Wei Peng / Marcela de Souza Santos / Yang Li / Diana R Tomchick / Kim Orth /
Abstract: Pore-forming proteins (PFPs) represent a functionally important protein family, that are found in organisms from viruses to humans. As a major branch of PFPs, bacteria pore-forming toxins (PFTs) ...Pore-forming proteins (PFPs) represent a functionally important protein family, that are found in organisms from viruses to humans. As a major branch of PFPs, bacteria pore-forming toxins (PFTs) permeabilize membranes and usually cause the death of target cells. E. coli hemolysin ClyA is the first member with the pore complex structure solved among α-PFTs, employing α-helices as transmembrane elements. ClyA is proposed to form pores composed of various numbers of protomers. With high-resolution cryo-EM structures, we observe that ClyA pore complexes can exist as newly confirmed oligomers of a tridecamer and a tetradecamer, at estimated resolutions of 3.2 Å and 4.3 Å, respectively. The 2.8 Å cryo-EM structure of a dodecamer dramatically improves the existing structural model. Structural analysis indicates that protomers from distinct oligomers resemble each other and neighboring protomers adopt a conserved interaction mode. We also show a stabilized intermediate state of ClyA during the transition process from soluble monomers to pore complexes. Unexpectedly, even without the formation of mature pore complexes, ClyA can permeabilize membranes and allow leakage of particles less than ~400 Daltons. In addition, we are the first to show that ClyA forms pore complexes in the presence of cholesterol within artificial liposomes. These findings provide new mechanistic insights into the dynamic process of pore assembly for the prototypical α-PFT ClyA.
Validation ReportPDB-ID: 6mrt

SummaryFull reportAbout validation report
DepositionOct 15, 2018-
Header (metadata) releaseNov 14, 2018-
Map releaseMay 15, 2019-
UpdateMay 15, 2019-
Current statusMay 15, 2019Processing site: RCSB / Status: Released

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6mrt
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
Supplemental images

Downloads & links


FileDownload / File: emd_9212.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 280 pix.
= 299.6 Å
1.07 Å/pix.
x 280 pix.
= 299.6 Å
1.07 Å/pix.
x 280 pix.
= 299.6 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Contour LevelBy AUTHOR: 0.07 / Movie #1: 0.07
Minimum - Maximum-0.16475789 - 0.2876716
Average (Standard dev.)-0.000038038674 (±0.010210648)
SymmetrySpace group: 1


Map geometry
Axis orderXYZ
CellA=B=C: 299.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z299.600299.600299.600
start NX/NY/NZ000
MAP C/R/S123
start NC/NR/NS000
D min/max/mean-0.1650.288-0.000

Supplemental data

Sample components

Entire 12-meric ClyA pore complex

EntireName: 12-meric ClyA pore complex / Number of components: 2

Component #1: protein, 12-meric ClyA pore complex

ProteinName: 12-meric ClyA pore complex / Recombinant expression: No
MassExperimental: 410 kDa
SourceSpecies: Escherichia coli (E. coli)
Source (engineered)Expression System: Escherichia coli (E. coli)

Component #2: protein, Hemolysin E, chromosomal

ProteinName: Hemolysin E, chromosomal / Number of Copies: 12 / Recombinant expression: No
MassTheoretical: 36.131816 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria) / Strain: K12
Source (engineered)Expression System: Escherichia coli (E. coli)

Experimental details

Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 8
Support filmunspecified
VitrificationCryogen name: ETHANE

Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 50 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 482946
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF

Atomic model buiding

Output model

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