9DCR | pdb_00009dcr

Structure of the TelA-associated type VII secretion system chaperone SIR_0168


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 
    0.244 (Depositor), 0.243 (DCC) 
  • R-Value Work: 
    0.195 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 
    0.197 (Depositor) 

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9DCR

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: 54.29 kDa 
  • Atom Count: 3,722 
  • Modeled Residue Count: 429 
  • Deposited Residue Count: 466 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DUF4176 domain-containing protein
A, B
233Streptococcus intermedius B196Mutation(s): 0 
Gene Names: SIR_0168
UniProt
Find proteins for T1ZCF9 (Streptococcus intermedius B196)
Explore T1ZCF9 
Go to UniProtKB:  T1ZCF9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupT1ZCF9
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free:  0.244 (Depositor), 0.243 (DCC) 
  • R-Value Work:  0.195 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 0.197 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.76α = 90
b = 63.49β = 101.55
c = 111.99γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
HKL-3000phasing
MOLREPphasing

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