9CCP | pdb_00009ccp

Cryo-EM structure of the EaCDCL pore


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.87 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9CCP

This is version 1.0 of the entry. See complete history

Literature

Structural basis for the pore-forming activity of a complement-like toxin.

Johnstone, B.A.Christie, M.P.Joseph, R.Morton, C.J.Brown, H.G.Hanssen, E.Sanford, T.C.Abrahamsen, H.L.Tweten, R.K.Parker, M.W.

(2025) Sci Adv 11: eadt2127-eadt2127

  • DOI: https://doi.org/10.1126/sciadv.adt2127
  • Primary Citation Related Structures: 
    8G33, 9CCP, 9CCQ

  • PubMed Abstract: 

    Pore-forming proteins comprise a highly diverse group of proteins exemplified by the membrane attack complex/perforin (MACPF), cholesterol-dependent cytolysin (CDC), and gasdermin superfamilies, which all form gigantic pores (>150 angstroms). A recently found family of pore-forming toxins, called CDC-like proteins (CDCLs), are wide-spread in gut microbes and are a prevalent means of antibacterial antagonism. However, the structural aspects of how CDCLs assemble a pore remain a mystery. Here, we report the crystal structure of a proteolytically activated CDCL and cryo-electron microscopy structures of a prepore-like intermediate and a transmembrane pore providing detailed snapshots across the entire pore-forming pathway. These studies reveal a sophisticated array of regulatory features to ensure productive pore formation, and, thus, CDCLs straddle the MACPF, CDC, and gasdermin lineages of the giant pore superfamilies.


  • Organizational Affiliation
    • Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3010, Australia.

Macromolecule Content 

  • Total Structure Weight: 1,186.02 kDa 
  • Atom Count: 58,080 
  • Modeled Residue Count: 7,590 
  • Deposited Residue Count: 10,860 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Thiol-activated cytolysin family protein
A, AA, B, BA, C
A, AA, B, BA, C, CA, D, DA, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z
362Elizabethkingia anophelis Ag1Mutation(s): 0 
Gene Names: JCR23_19030

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CA

Query on CA



Download:Ideal Coordinates CCD File
AB [auth W]
BB [auth X]
CB [auth Y]
DB [auth Z]
EA [auth A]
AB [auth W],
BB [auth X],
CB [auth Y],
DB [auth Z],
EA [auth A],
EB [auth AA],
FA [auth B],
FB [auth BA],
GA [auth C],
GB [auth CA],
HA [auth D],
HB [auth DA],
IA [auth E],
JA [auth F],
KA [auth G],
LA [auth H],
MA [auth I],
NA [auth J],
OA [auth K],
PA [auth L],
QA [auth M],
RA [auth N],
SA [auth O],
TA [auth P],
UA [auth Q],
VA [auth R],
WA [auth S],
XA [auth T],
YA [auth U],
ZA [auth V]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.87 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Australian Research Council (ARC)AustraliaDP160101874
Australian Research Council (ARC)AustraliaDP200102871
National Health and Medical Research Council (NHMRC, Australia)AustraliaAPP1194263

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-09
    Type: Initial release