9MNO | pdb_00009mno

Structure of the TelA-associated type VII secretion system chaperone LcpA in complex with the chaperone binding site of TelA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 
    0.243 (Depositor), 0.243 (DCC) 
  • R-Value Work: 
    0.204 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 
    0.206 (Depositor) 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


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 of 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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DUF4176 domain-containing protein
A, B, C, D
219Streptococcus 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
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
LXG domain-containing protein
E, F, G
64Streptococcus intermedius B196Mutation(s): 0 
Gene Names: SIR_0169
UniProt
Find proteins for T1ZCZ9 (Streptococcus intermedius B196)
Explore T1ZCZ9 
Go to UniProtKB:  T1ZCZ9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupT1ZCZ9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download Ideal Coordinates CCD File 
H [auth D]CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free:  0.243 (Depositor), 0.243 (DCC) 
  • R-Value Work:  0.204 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 0.206 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.822α = 99.943
b = 54.855β = 96.421
c = 119.922γ = 90.785
Software Package:
Software NamePurpose
PHENIXrefinement
AutoProcessdata reduction
Aimlessdata scaling
HKL-3000phasing
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)CanadaPJT-173486
European Molecular Biology Organization (EMBO)European UnionALTF 139-2024

Revision History  (Full details and data files)

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