6ZD0

Disulfide-locked early prepore intermedilysin-CD59


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis for tuning activity and membrane specificity of bacterial cytolysins.

Shah, N.R.Voisin, T.B.Parsons, E.S.Boyd, C.M.Hoogenboom, B.W.Bubeck, D.

(2020) Nat Commun 11: 5818-5818

  • DOI: https://doi.org/10.1038/s41467-020-19482-6
  • Primary Citation of Related Structures:  
    6ZD0

  • PubMed Abstract: 

    Cholesterol-dependent cytolysins (CDCs) are pore-forming proteins that serve as major virulence factors for pathogenic bacteria. They target eukaryotic cells using different mechanisms, but all require the presence of cholesterol to pierce lipid bilayers. How CDCs use cholesterol to selectively lyse cells is essential for understanding virulence strategies of several pathogenic bacteria, and for repurposing CDCs to kill new cellular targets. Here we address that question by trapping an early state of pore formation for the CDC intermedilysin, bound to the human immune receptor CD59 in a nanodisc model membrane. Our cryo electron microscopy map reveals structural transitions required for oligomerization, which include the lateral movement of a key amphipathic helix. We demonstrate that the charge of this helix is crucial for tuning lytic activity of CDCs. Furthermore, we discover modifications that overcome the requirement of cholesterol for membrane rupture, which may facilitate engineering the target-cell specificity of pore-forming proteins.


  • Organizational Affiliation

    Department of Life Sciences, Sir Ernst Chain Building, Imperial College London, London, SW7 2AZ, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thiol-activated cytolysin
A, C, E
535Streptococcus intermediusMutation(s): 2 
Gene Names: ily
UniProt
Find proteins for Q9LCB8 (Streptococcus intermedius)
Explore Q9LCB8 
Go to UniProtKB:  Q9LCB8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9LCB8
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CD59 glycoprotein
B, D, F
79Homo sapiensMutation(s): 0 
Gene Names: CD59MIC11MIN1MIN2MIN3MSK21
UniProt & NIH Common Fund Data Resources
Find proteins for P13987 (Homo sapiens)
Explore P13987 
Go to UniProtKB:  P13987
PHAROS:  P13987
GTEx:  ENSG00000085063 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13987
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cancer Research UKUnited KingdomC26409/A16099

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-18
    Type: Initial release
  • Version 1.1: 2020-11-25
    Changes: Database references
  • Version 1.2: 2024-05-01
    Changes: Data collection, Database references, Refinement description