8AKO

Structure of EspB-EspK complex: the non-identical twin of the PE-PPE-EspG secretion mechanism.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.235 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The crystal structure of the EspB-EspK virulence factor-chaperone complex suggests an additional type VII secretion mechanism in Mycobacterium tuberculosis.

Gijsbers, A.Eymery, M.Gao, Y.Menart, I.Vinciauskaite, V.Siliqi, D.Peters, P.J.McCarthy, A.Ravelli, R.B.G.

(2022) J Biol Chem 299: 102761-102761

  • DOI: https://doi.org/10.1016/j.jbc.2022.102761
  • Primary Citation of Related Structures:  
    8AKO

  • PubMed Abstract: 

    Pathogenic species from the Mycobacterium genus are responsible for a number of adverse health conditions in humans and animals that threaten health security and the economy worldwide. Mycobacteria have up to five specialized secretion systems (ESX-1 to ESX-5) that transport virulence factors across their complex cell envelope to facilitate manipulation of their environment. In pathogenic species, these virulence factors influence the immune system's response and are responsible for membrane disruption and contributing to cell death. While structural details of these secretion systems have been recently described, gaps still remain in the structural understanding of the secretion mechanisms of most substrates. Here, we describe the crystal structure of Mycobacterium tuberculosis ESX-1 secretion-associated substrate EspB bound to its chaperone EspK. We found that EspB interacts with the C-terminal domain of EspK through its helical tip. Furthermore, cryogenic electron microscopy, size exclusion chromatography analysis, and small-angle X-ray scattering experiments show that EspK keeps EspB in its secretion-competent monomeric form and prevents its oligomerization. The structure presented in this study suggests an additional secretion mechanism in ESX-1, analogous to the chaperoning of proline-glutamate (PE)-proline-proline-glutamate (PPE) proteins by EspG, where EspK facilitates the secretion of EspB in Mycobacterium species.


  • Organizational Affiliation

    Division of Nanoscopy, Maastricht Multimodal Molecular Imaging Institute (M4i), Maastricht University, Maastricht, the Netherlands.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ESX-1 secretion-associated protein EspB300Mycobacterium tuberculosisMutation(s): 0 
Gene Names: espBmtb48Rv3881cMTV027.16c
UniProt
Find proteins for P9WJD9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WJD9 
Go to UniProtKB:  P9WJD9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WJD9
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ESX-1 secretion-associated protein EspK246Mycobacterium tuberculosisMutation(s): 0 
Gene Names: espKRv3879c
UniProt
Find proteins for P9WJC1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WJC1 
Go to UniProtKB:  P9WJC1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WJC1
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.235 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.579α = 90
b = 101.579β = 90
c = 377.045γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Netherlands Organisation for Scientific Research (NWO)Netherlands731.016.407
Netherlands Organisation for Scientific Research (NWO)Netherlands184.034.014
European Union (EU)European Union766970
French Infrastructure for Integrated Structural Biology (FRISBI)FranceANR-10-INBS-05-02

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-14
    Type: Initial release
  • Version 1.1: 2023-01-11
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description