6EHB

OmpU, an outer membrane protein, of Vibrio cholerae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 

wwPDB Validation 3D Report Full Report


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: 10.1016/j.str.2018.03.010
  • Structures With Same Primary Citation

  • 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 Enterobacteriacea ...

    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. Electronic address: bert.van-den-berg@ncl.ac.uk.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Outer membrane protein U
A, B, C
320Vibrio cholerae O395Mutation(s): 0 
Gene Names: ompUVC0395_A0162VC395_0650
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: BETA-BARREL
Sub Group: 
Beta-Barrel Membrane Proteins: Porins and Relatives
Protein: 
OmpU porin
Find proteins for A5F934 (Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395))
Go to UniProtKB:  A5F934
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
C8E
Query on C8E

Download CCD File 
A, B, C
(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
C16 H34 O5
FEOZZFHAVXYAMB-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.723α = 90
b = 153.84β = 102.32
c = 66.17γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Innovative Medicines Initiatives Joint UndertakingUnited Kingdom115525

Revision History 

  • 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