Pilotin from Vibrio vulnificus type 2 secretion system, EpsS.

Experimental Data Snapshot

  • Resolution: 1.75 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.185 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Structure and assembly of pilotin-dependent and -independent secretins of the type II secretion system.

Howard, S.P.Estrozi, L.F.Bertrand, Q.Contreras-Martel, C.Strozen, T.Job, V.Martins, A.Fenel, D.Schoehn, G.Dessen, A.

(2019) PLoS Pathog 15: e1007731-e1007731

  • DOI: https://doi.org/10.1371/journal.ppat.1007731
  • Primary Citation of Related Structures:  
    6I1X, 6I1Y, 6I2V

  • PubMed Abstract: 

    The type II secretion system (T2SS) is a cell envelope-spanning macromolecular complex that is prevalent in Gram-negative bacterial species. It serves as the predominant virulence mechanism of many bacteria including those of the emerging human pathogens Vibrio vulnificus and Aeromonas hydrophila. The system is composed of a core set of highly conserved proteins that assemble an inner membrane platform, a periplasmic pseudopilus and an outer membrane complex termed the secretin. Localization and assembly of secretins in the outer membrane requires recognition of secretin monomers by two different partner systems: an inner membrane accessory complex or a highly sequence-diverse outer membrane lipoprotein, termed the pilotin. In this study, we addressed the question of differential secretin assembly mechanisms by using cryo-electron microscopy to determine the structures of the secretins from A. hydrophila (pilotin-independent ExeD) and V. vulnificus (pilotin-dependent EpsD). These structures, at approximately 3.5 Å resolution, reveal pentadecameric stoichiometries and C-terminal regions that carry a signature motif in the case of a pilotin-dependent assembly mechanism. We solved the crystal structure of the V. vulnificus EpsS pilotin and confirmed the importance of the signature motif for pilotin-dependent secretin assembly by performing modelling with the C-terminus of EpsD. We also show that secretin assembly is essential for membrane integrity and toxin secretion in V. vulnificus and establish that EpsD requires the coordinated activity of both the accessory complex EpsAB and the pilotin EpsS for full assembly and T2SS function. In contrast, mutation of the region of the S-domain that is normally the site of pilotin interactions has little effect on assembly or function of the ExeD secretin. Since secretins are essential outer membrane channels present in a variety of secretion systems, these results provide a structural and functional basis for understanding the key assembly steps for different members of this vast pore-forming family of proteins.

  • Organizational Affiliation

    Dept. Biochemistry, Microbiology and Immunology, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein114Vibrio vulnificusMutation(s): 0 
Gene Names: CRN52_08940CRN59_22290FORC17_1995FORC36_0970
Find proteins for A0A1V8MYF4 (Vibrio vulnificus)
Explore A0A1V8MYF4 
Go to UniProtKB:  A0A1V8MYF4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1V8MYF4
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 1PE

Download Ideal Coordinates CCD File 
B [auth A],
E [auth A],
F [auth A],
G [auth A],
I [auth A]
C10 H22 O6
Query on SO4

Download Ideal Coordinates CCD File 
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A]
O4 S
Query on SO3

Download Ideal Coordinates CCD File 
O3 S
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A],
H [auth A]
C2 H6 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 1.75 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.185 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.83α = 90
b = 83.21β = 90
c = 90.79γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-10
    Type: Initial release
  • Version 1.1: 2019-08-28
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description