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- PDB-6mrt: 12-meric ClyA pore complex -

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Database: PDB / ID: 6mrt
Title12-meric ClyA pore complex
ComponentsHemolysin E, chromosomal
KeywordsMEMBRANE PROTEIN / Toxin / Pore-forming toxin
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 / Haemolysin E (HlyE) / Hemolysin E; Chain: A; / Hemolysin E; Chain: A; - #10 / Up-down Bundle / Mainly Alpha
Hemolysin E, chromosomal
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsPeng, W. / de Souza Santos, M. / Li, Y. / Tomchick, D.R. / 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 Report
SummaryFull reportAbout validation report
DepositionOct 15, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2019Provider: repository / Type: Initial release

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Deposited unit
A: Hemolysin E, chromosomal
B: Hemolysin E, chromosomal
C: Hemolysin E, chromosomal
D: Hemolysin E, chromosomal
E: Hemolysin E, chromosomal
F: Hemolysin E, chromosomal
G: Hemolysin E, chromosomal
H: Hemolysin E, chromosomal
I: Hemolysin E, chromosomal
J: Hemolysin E, chromosomal
K: Hemolysin E, chromosomal
L: Hemolysin E, chromosomal

Theoretical massNumber of molelcules
Total (without water)433,58212

TypeNameSymmetry operationNumber
identity operation1_5551


#1: Protein
Hemolysin E, chromosomal / Cytotoxin ClyA / Hemolysis-inducing protein / Latent pore-forming 34 kDa hemolysin / Silent hemolysin SheA

Mass: 36131.816 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: hlyE, clyA, hpr, sheA, ycgD, b1182, JW5181 / Production host: Escherichia coli (E. coli) / References: UniProt: P77335

Experimental details


EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

Sample preparation

ComponentName: 12-meric ClyA pore complex / Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
Molecular weightValue: 0.41 MDa / Experimental value: YES
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationCryogen name: ETHANE

Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)


CTF correctionType: NONE
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 482946 / Symmetry type: POINT

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