Trimeric OmpU structure

Experimental Data Snapshot

  • Resolution: 2.22 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.209 

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This is version 1.4 of the entry. See complete history


Crystal structure of the outer membrane protein OmpU from Vibrio cholerae at 2.2 angstrom resolution.

Li, H.Zhang, W.Dong, C.

(2018) Acta Crystallogr D Struct Biol 74: 21-29

  • DOI: https://doi.org/10.1107/S2059798317017697
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Vibrio cholerae causes a severe disease that kills thousands of people annually. The outer membrane protein OmpU is the most abundant outer membrane protein in V. cholerae, and has been identified as an important virulence factor that is involved in host-cell interaction and recognition, as well as being critical for the survival of the pathogenic V. cholerae in the host body and in harsh environments. The mechanism of these processes is not well understood owing to a lack of the structure of V. cholerae OmpU. Here, the crystal structure of the V. cholerae OmpU trimer is reported to a resolution of 2.2 Å. The protomer forms a 16-β-stranded barrel with a noncanonical N-terminal coil located in the lumen of the barrel that consists of residues Gly32-Ser42 and is observed to participate in forming the second gate in the pore. By mapping the published functional data onto the OmpU structure, the OmpU structure reinforces the notion that the long extracellular loop L4 with a β-hairpin-like motif may be critical for host-cell binding and invasion, while L3, L4 and L8 are crucially implicated in phage recognition by V. cholerae.

  • Organizational Affiliation

    Biomedical Research Centre, Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, England.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Outer membrane protein OmpU
A, B, C
356Vibrio choleraeMutation(s): 0 
Gene Names: B2J67_03320B2J68_03135B2J70_03210B2J71_03065BTY66_11390CEF09_10965
Membrane Entity: Yes 
Find proteins for P0C6Q6 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
Explore P0C6Q6 
Go to UniProtKB:  P0C6Q6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C6Q6
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on C8E

Download Ideal Coordinates CCD File 
D [auth A],
J [auth B],
Q [auth C]
C16 H34 O5
Query on LDA

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
M [auth B]
N [auth B]
G [auth A],
H [auth A],
I [auth A],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
T [auth C],
U [auth C],
V [auth C]
C14 H31 N O
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
K [auth B]
L [auth B]
R [auth C]
E [auth A],
F [auth A],
K [auth B],
L [auth B],
R [auth C],
S [auth C]
C3 H8 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 2.22 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.209 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 129.88α = 90
b = 153.47β = 90
c = 81.01γ = 90
Software Package:
Software NamePurpose
iMOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-03
    Type: Initial release
  • Version 1.1: 2018-02-07
    Changes: Database references
  • Version 1.2: 2018-12-19
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.3: 2019-10-16
    Changes: Data collection
  • Version 1.4: 2024-05-08
    Changes: Data collection, Database references