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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-9214 | |||||||||
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Title | 14-meric ClyA pore complex | |||||||||
![]() | Tetradecamer | |||||||||
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![]() | Pore-forming toxin / MEMBRANE PROTEIN / Toxin | |||||||||
Function / homology | ![]() 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 | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.3 Å | |||||||||
![]() | Peng W / de Souza Santos M | |||||||||
![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 78.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 8.8 KB 8.8 KB | Display Display | ![]() |
Images | ![]() | 46.2 KB | ||
Filedesc metadata | ![]() | 5.2 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6mrwMC ![]() 9212C ![]() 9213C ![]() 6mrtC ![]() 6mruC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | Tetradecamer | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : 14-meric ClyA pore complex
Entire | Name: 14-meric ClyA pore complex |
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Components |
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-Supramolecule #1: 14-meric ClyA pore complex
Supramolecule | Name: 14-meric ClyA pore complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 480 KDa |
-Macromolecule #1: Hemolysin E, chromosomal
Macromolecule | Name: Hemolysin E, chromosomal / type: protein_or_peptide / ID: 1 / Number of copies: 14 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 36.131816 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 8 |
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Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: PDB ENTRY |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 30904 |
Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: NOT APPLICABLE |