8G32 | pdb_00008g32

Pro-form of a CDCL short from E. anophelis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 
    0.180 (Depositor), 0.180 (DCC) 
  • R-Value Work: 
    0.162 (Depositor), 0.161 (DCC) 
  • R-Value Observed: 
    0.162 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8G32

This is version 1.2 of the entry. See complete history

Literature

Distant relatives of a eukaryotic cell-specific toxin family evolved a complement-like mechanism to kill bacteria.

Abrahamsen, H.L.Sanford, T.C.Collamore, C.E.Johnstone, B.A.Coyne, M.J.Garcia-Bayona, L.Christie, M.P.Evans, J.C.Farrand, A.J.Flores, K.Morton, C.J.Parker, M.W.Comstock, L.E.Tweten, R.K.

(2024) Nat Commun 15: 5028-5028

  • DOI: https://doi.org/10.1038/s41467-024-49103-5
  • Primary Citation Related Structures: 
    8G32

  • PubMed Abstract: 

    Cholesterol-dependent cytolysins (CDCs) comprise a large family of pore-forming toxins produced by Gram-positive bacteria, which are used to attack eukaryotic cells. Here, we functionally characterize a family of 2-component CDC-like (CDCL) toxins produced by the Gram-negative Bacteroidota that form pores by a mechanism only described for the mammalian complement membrane attack complex (MAC). We further show that the Bacteroides CDCLs are not eukaryotic cell toxins like the CDCs, but instead bind to and are proteolytically activated on the surface of closely related species, resulting in pore formation and cell death. The CDCL-producing Bacteroides is protected from the effects of its own CDCL by the presence of a surface lipoprotein that blocks CDCL pore formation. These studies suggest a prevalent mode of bacterial antagonism by a family of two-component CDCLs that function like mammalian MAC and that are wide-spread in the gut microbiota of diverse human populations.


  • Organizational Affiliation
    • Department of Microbiology & Immunology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.

Macromolecule Content 

  • Total Structure Weight: 79.88 kDa 
  • Atom Count: 5,474 
  • Modeled Residue Count: 646 
  • Deposited Residue Count: 724 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Thiol-activated cytolysin family protein
A, B
362Elizabethkingia anophelis Ag1Mutation(s): 0 
Gene Names: JCR23_19030
UniProt
Find proteins for A0A1T3D3K1 (Elizabethkingia anophelis)
Explore A0A1T3D3K1 
Go to UniProtKB:  A0A1T3D3K1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1T3D3K1
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PG4

Query on PG4



Download:Ideal Coordinates CCD File
F [auth A]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
C [auth A],
J [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
D [auth A],
K [auth B],
L [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
E [auth A],
G [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
H [auth A],
M [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
I [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free:  0.180 (Depositor), 0.180 (DCC) 
  • R-Value Work:  0.162 (Depositor), 0.161 (DCC) 
  • R-Value Observed: 0.162 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 171.629α = 90
b = 171.629β = 90
c = 61.334γ = 120
Software Package:
Software NamePurpose
DIALSdata reduction
xia2data reduction
Aimlessdata scaling
PHASERphasing
PHENIXmodel building
Cootmodel building
PHENIXrefinement

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

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-07
    Type: Initial release
  • Version 1.1: 2024-06-19
    Changes: Database references
  • Version 1.2: 2024-06-26
    Changes: Database references