8G33 | pdb_00008g33

Activated form of a CDCL long protein

• PDB DOI: https://doi.org/10.2210/pdb8G33/pdb

• Classification: TOXIN
• Organism(s): Elizabethkingia anophelis Ag1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-02-06 Released: 2024-02-07 
• Deposition Author(s): Johnstone, B.A., Christie, M.P., Morton, C.J., Parker, M.W.
• Funding Organization(s): Australian Research Council (ARC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free: 
  0.248 (Depositor), 0.248 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Starting Model: experimental

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

• PubMed: 40153490 
• 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.

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Organizational Affiliation: 
• Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3010, Australia.
ARC Centre for Cryo-Electron Microscopy of Membrane Proteins, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3010, Australia.
Ian Holmes Imaging Centre, Bio21 Molecular Science & Biotechnology Institute, University of Melbourne, Parkville, VIC 3010, Australia.
Department of Microbiology & Immunology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
Australian Cancer Research Foundation Rational Drug Discovery Centre, St Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: SAXS, gel filtration, light scattering

Macromolecule Content 

• Total Structure Weight: 55.91 kDa 
• Atom Count: 3,537 
• Modeled Residue Count: 436 
• Deposited Residue Count: 497 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemolysin	A	497	Elizabethkingia anophelis Ag1	Mutation(s): 0  Gene Names: ply_2, AYC66_13765, BAY09_14710, NCTC10586_03727
UniProt
Find proteins for A0A1T3IZT7 (Elizabethkingia anophelis) Explore A0A1T3IZT7  Go to UniProtKB:  A0A1T3IZT7

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free:  0.248 (Depositor), 0.248 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.725	α = 90
b = 24.451	β = 93.19
c = 300.191	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
Coot	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-02-07 
Deposition Author(s): Johnstone, B.A., Christie, M.P., Morton, C.J., Parker, M.W.

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Funding Organization	Location	Grant Number
Australian Research Council (ARC)	Australia	DP200102871
Australian Research Council (ARC)	Australia	DP160101874

Revision History  

• Version 1.0: 2024-02-07
  Type: Initial release
  
• Version 1.1: 2025-04-09
  Changes: Database references, Structure summary