8ARB

Heterologous Complex of shortened Aeromonas hydrophila Type III secretion substrate AscX with Yersinia enterocolitica chaperone YscY


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.63 Å
  • R-Value Free: 0.326 
  • R-Value Work: 0.291 
  • R-Value Observed: 0.293 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The type III secretion chaperone SctY may shield the hydrophobic export gate-binding C-terminus of its substrate SctX.

Gilzer, D.Kowal, J.L.Flottmann, F.Niemann, H.H.

(2023) Acta Crystallogr D Struct Biol 79: 508-517

  • DOI: https://doi.org/10.1107/S2059798323003248
  • Primary Citation of Related Structures:  
    8ARA, 8ARB, 8ARC

  • PubMed Abstract: 

    Gram-negative bacteria such as Aeromonas and Yersinia spp. have developed mechanisms to inhibit the immune defense of their host. Effector proteins are directly injected into the host cytoplasm from the bacterial cytosol via type III secretion systems (T3SSs), where they modulate the cytoskeleton and signaling of the cell. Assembly of, and secretion via, T3SSs is tightly regulated by a number of bacterial proteins, including SctX (AscX in Aeromonas), the secretion of which is essential for T3SS function. Here, crystal structures of AscX in complex with SctY chaperones from Yersinia or Photorhabdus spp. carrying homologous T3SSs are described. There are crystal pathologies in all cases, with one crystal form diffracting anisotropically and the other two exhibiting strong pseudotranslation. The new structures reveal that the positioning of the substrate is very similar on different chaperones. However, the two C-terminal SctX helices that cap the N-terminal tetratricopeptide repeat of SctY shift and tilt depending on the identity of the chaperone. Moreover, the C-terminus of the α3 helix of AscX exhibits an unprecedented kink in two of the structures. In previous structures, the C-terminus of SctX protrudes beyond the chaperone as a straight helix: a conformation that is required for binding to the nonameric export gate SctV but that is unfavorable for binary SctX-SctY complexes due to the hydrophobicity of helix α3 of SctX. A kink in helix α3 may allow the chaperone to shield the hydrophobic C-terminus of SctX in solution.


  • Organizational Affiliation

    Department of Chemistry, Bielefeld University, Universitaetsstrasse 25, 33615 Bielefeld, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chaperone protein YscY
A, C, E, G
122Yersinia enterocoliticaMutation(s): 0 
Gene Names: yscY
UniProt
Find proteins for P0C2N2 (Yersinia enterocolitica)
Explore P0C2N2 
Go to UniProtKB:  P0C2N2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C2N2
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
AscX
B, D, F, H
76Aeromonas hydrophilaMutation(s): 0 
Gene Names: ascX
UniProt
Find proteins for Q699R5 (Aeromonas hydrophila)
Explore Q699R5 
Go to UniProtKB:  Q699R5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ699R5
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.33α = 90
b = 160.56β = 90
c = 156.74γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-26
    Type: Initial release
  • Version 1.1: 2023-06-21
    Changes: Database references
  • Version 1.2: 2024-02-07
    Changes: Data collection, Refinement description