OmpT (in-vitro folded), an outer membrane protein Vibrio cholerae (trimer form)

Experimental Data Snapshot

  • Resolution: 2.72 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.240 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
OmpT protein319Vibrio cholerae O395Mutation(s): 1 
Gene Names: ompTVC0395_A1445
Membrane Entity: Yes 
Find proteins for A0A0H3AME7 (Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395))
Explore A0A0H3AME7 
Go to UniProtKB:  A0A0H3AME7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H3AME7
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on CA

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

  • Resolution: 2.72 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.240 
  • Space Group: I 4 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 200.91α = 90
b = 200.91β = 90
c = 200.91γ = 90
Software Package:
Software NamePurpose
xia2data reduction
xia2data scaling

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: 2018-10-03
    Changes: Data collection
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Refinement description