periplasmic domain of EpsL from Vibrio parahaemolyticus

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 

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This is version 1.2 of the entry. See complete history


The Dimer Formed by the Periplasmic Domain of Epsl from the Type 2 Secretion System of Vibrio Parahaemolyticus.

Abendroth, J.Kreger, A.C.Hol, W.G.J.

(2009) J Struct Biol 168: 313

  • DOI: https://doi.org/10.1016/j.jsb.2009.07.022
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The Type 2 Secretion System (T2SS), occurring in many Gram-negative bacteria, is responsible for the transport of a diversity of proteins from the periplasm across the outer membrane into the extracellular space. In Vibrio cholerae, the T2SS secretes several unrelated proteins including the major virulence factor cholera toxin. The T2SS consists of three sub-assemblies, one of which is the Inner Membrane Complex which contains multiple copies of five proteins, including the bitopic membrane protein EpsL. Here, we report the 2.3A resolution crystal structure of the periplasmic domain of EpsL (peri-EpsL) from Vibrio parahaemolyticus, which is 56% identical in sequence to its homolog in V. cholerae. The domain adopts a circular permutation of the "common" ferredoxin fold with two contiguous sub-domains. Remarkably, this infrequently occurring permutation was for the first time observed in the periplasmic domain of EpsM (peri-EpsM), another T2SS protein which interacts with EpsL. These two domains are 18% identical in sequence which may indicate a common evolutionary origin. Both peri-EpsL and peri-EpsM form dimers, but the organization of the subunits in these dimers appears to be entirely different. We have previously shown that the cytoplasmic domain of EpsL is also dimeric and forms a heterotetramer with the first domain of the "secretion ATPase" EpsE. The latter enzyme is most likely hexameric. The possible consequences of the combination of the different symmetries of EpsE and EpsL for the architecture of the T2SS are discussed.

  • Organizational Affiliation

    Department of Biochemistry, Biomolecular Structure Center, University of Washington, Seattle, 98195, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
95Vibrio parahaemolyticusMutation(s): 0 
Find proteins for Q87TC9 (Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633))
Explore Q87TC9 
Go to UniProtKB:  Q87TC9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ87TC9
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 
  • Space Group: P 62
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.712α = 90
b = 87.712β = 90
c = 45.589γ = 120
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-03-31
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2017-06-28
    Changes: Refinement description