5OYK

Outer-membrane expressed OmpT of Vibrio cholerae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Unusual Constriction Zones in the Major Porins OmpU and OmpT from Vibrio cholerae.

Pathania, M.Acosta-Gutierrez, S.Bhamidimarri, S.P.Basle, A.Winterhalter, M.Ceccarelli, M.van den Berg, B.

(2018) Structure 26: 708-721.e4

  • DOI: https://doi.org/10.1016/j.str.2018.03.010
  • Primary Citation of Related Structures:  
    5OYK, 6EHB, 6EHC, 6EHD, 6EHE, 6EHF

  • PubMed Abstract: 

    The outer membranes (OM) of many Gram-negative bacteria contain general porins, which form nonspecific, large-diameter channels for the diffusional uptake of small molecules required for cell growth and function. While the porins of Enterobacteriaceae (e.g., E. coli OmpF and OmpC) have been extensively characterized structurally and biochemically, much less is known about their counterparts in Vibrionaceae. Vibrio cholerae, the causative agent of cholera, has two major porins, OmpU and OmpT, for which no structural information is available despite their importance for the bacterium. Here we report high-resolution X-ray crystal structures of V. cholerae OmpU and OmpT complemented with molecular dynamics simulations. While similar overall to other general porins, the channels of OmpU and OmpT have unusual constrictions that create narrower barriers for small-molecule permeation and change the internal electric fields of the channels. Together with electrophysiological and in vitro transport data, our results illuminate small-molecule uptake within the Vibrionaceae.


  • Organizational Affiliation

    Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle Upon Tyne NE2 4HH, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Gram-negative porin family protein325Vibrio choleraeMutation(s): 0 
Gene Names: ompTDN30_688EN12_08995ERS013173_00485ERS013186_03149ERS013197_04241ERS013198_02336ERS013201_00314ERS013202_01691
Membrane Entity: Yes 
UniProt
Find proteins for O86021 (Vibrio cholerae)
Explore O86021 
Go to UniProtKB:  O86021
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO86021
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.61α = 90
b = 74.33β = 96.74
c = 62.31γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Innovative Medicines Initiatives Joint UndertakingUnited Kingdom115525

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-25
    Type: Initial release
  • Version 1.1: 2018-05-09
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description