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- EMDB-9213: 13-meric ClyA pore complex -

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Basic information

Entry
Database: EMDB / ID: EMD-9213
Title13-meric ClyA pore complex
Map dataTridecamer
Sample
  • Complex: 13-meric ClyA pore complex
    • Protein or peptide: Hemolysin E, chromosomal
KeywordsPore-forming toxin / MEMBRANE PROTEIN / Toxin
Function / homology
Function and homology information


modulation of apoptotic process in another organism / hemolysis in another organism / toxin activity / periplasmic space / host cell plasma membrane / extracellular region / identical protein binding / membrane
Similarity search - Function
Hemolysin E / Haemolysin E (HlyE)
Similarity search - Domain/homology
Hemolysin E, chromosomal
Similarity search - Component
Biological speciesEscherichia coli (E. coli) / Escherichia coli (strain K12) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsPeng W / de Souza Santos M
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.
History
DepositionOct 15, 2018-
Header (metadata) releaseOct 24, 2018-
Map releaseMay 15, 2019-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6mru
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9213.png

Downloads & links

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Map

FileDownload / File: emd_9213.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTridecamer
Projections & slices

Image control

Size
Brightness
Contrast
Others
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

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.10034035 - 0.18288244
Average (Standard dev.)-0.000031085972 (±0.0070824474)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
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
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ208208208
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-0.1000.183-0.000

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Supplemental data

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Sample components

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Entire : 13-meric ClyA pore complex

EntireName: 13-meric ClyA pore complex
Components
  • Complex: 13-meric ClyA pore complex
    • Protein or peptide: Hemolysin E, chromosomal

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Supramolecule #1: 13-meric ClyA pore complex

SupramoleculeName: 13-meric ClyA pore complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 440 KDa

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Macromolecule #1: Hemolysin E, chromosomal

MacromoleculeName: Hemolysin E, chromosomal / type: protein_or_peptide / ID: 1 / Number of copies: 13 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 36.131816 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SQDLDEVDAG SMTEIVADKT VEVVKNAIET ADGALDLYNK YLDQVIPWQT FDETIKELSR FKQEYSQAAS VLVGDIKTL LMDSQDKYFE ATQTVYEWCG VATQLLAAYI LLFDEYNEKK ASAQKDILIK VLDDGITKLN EAQKSLLVSS Q SFNNASGK ...String:
MGSSHHHHHH SQDLDEVDAG SMTEIVADKT VEVVKNAIET ADGALDLYNK YLDQVIPWQT FDETIKELSR FKQEYSQAAS VLVGDIKTL LMDSQDKYFE ATQTVYEWCG VATQLLAAYI LLFDEYNEKK ASAQKDILIK VLDDGITKLN EAQKSLLVSS Q SFNNASGK LLALDSQLTN DFSEKSSYFQ SQVDKIRKEA YAGAAAGVVA GPFGLIISYS IAAGVVEGKL IPELKNKLKS VQ NFFTTLS NTVKQANKDI DAAKLKLTTE IVAIGEIKTE TETTRFYVDY DDLMLSLLKE AAKKMINTCN EYQKRHGKKT LFE VPEV

UniProtKB: Hemolysin E, chromosomal

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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

BufferpH: 8
GridDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 68997
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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