9DCS | pdb_00009dcs

Structure of a TelD-associated type VII secretion system DUF4176 protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.275 (Depositor), 0.267 (DCC) 
  • R-Value Work: 
    0.228 (Depositor), 0.228 (DCC) 
  • R-Value Observed: 
    0.230 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history

Literature

A widespread family of molecular chaperones promotes the intracellular stability of type VIIb secretion system-exported toxins.

Gkragkopoulou, P.Garrett, S.R.Shah, P.Y.Grebenc, D.W.Klein, T.A.Kim, Y.Whitney, J.C.

(2025) Proc Natl Acad Sci U S A 122: e2503581122-e2503581122

  • DOI: https://doi.org/10.1073/pnas.2503581122
  • Primary Citation Related Structures: 
    9DCR, 9DCS, 9DCT, 9MNO

  • PubMed Abstract: 

    To survive in highly competitive environments, bacteria use specialized secretion systems to deliver antibacterial toxins into neighboring cells, thereby inhibiting their growth. In many Gram-positive bacteria, the export of such toxins requires a membrane-bound molecular apparatus known as the type VIIb secretion system (T7SSb). Recently, it was shown that toxin recruitment to the T7SSb requires a physical interaction between a toxin and two or more so-called targeting factors, which harbor key residues required for T7SS-dependent protein export. However, in addition to these targeting factors, some toxins additionally require a protein belonging to the DUF4176 protein family. Here, by examining two toxin-DUF4176 protein pairs, we demonstrate that DUF4176 constitutes a family of toxin-specific molecular chaperones. In addition to being required for toxin stability in producing cells, we find that DUF4176 proteins facilitate toxin export by specifically interacting with a previously uncharacterized intrinsically disordered region found in many T7SS toxins. Using X-ray crystallography, we determine structures of several DUF4176 chaperones in their unbound state, and of a DUF4176 chaperone in complex with the binding site of its cognate toxin. These structures reveal that this binding site consists of a disordered amphipathic α-helix that requires interaction with its cognate chaperone for proper folding. Overall, we have identified a family of secretion system associated molecular chaperones found throughout T7SSb-containing Gram-positive bacteria.


  • Organizational Affiliation
    • Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4K1, Canada.

Macromolecule Content 

  • Total Structure Weight: 49.04 kDa 
  • Atom Count: 3,198 
  • Modeled Residue Count: 389 
  • Deposited Residue Count: 416 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DUF4176 domain-containing protein
A, B, C, D
104Streptococcus intermediusMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.275 (Depositor), 0.267 (DCC) 
  • R-Value Work:  0.228 (Depositor), 0.228 (DCC) 
  • R-Value Observed: 0.230 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.49α = 90
b = 82.49β = 90
c = 144.88γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
MLPHAREphasing
HKL-3000phasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)CanadaPJT-173486

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-05
    Type: Initial release