2CM4

The complement inhibitor OmCI in complex with ricinoleic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Work: 0.169 
  • R-Value Observed: 0.169 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Literature

The Structure of Omci, a Novel Lipocalin Inhibitor of the Complement System.

Roversi, P.Lissina, O.Johnson, S.Ahmat, N.Paesen, G.C.Ploss, K.Boland, W.Nunn, M.A.Lea, S.M.

(2007) J Mol Biol 369: 784

  • DOI: https://doi.org/10.1016/j.jmb.2007.03.064
  • Primary Citation of Related Structures:  
    2CM4, 2CM9

  • PubMed Abstract: 

    The complement (C) system is a potent innate immune defence system against parasites. We have recently characterised and expressed OmCI, a 16 kDa protein derived from the soft tick Ornithodoros moubata that specifically binds C5, thereby preventing C activation. The structure of recombinant OmCI determined at 1.9 A resolution confirms a lipocalin fold and reveals that the protein binds a fatty acid derivative that we have identified by mass spectrometry as ricinoleic acid. We propose that OmCI could sequester one of the fatty acid-derived inflammatory modulators from the host plasma, thereby interfering with the host inflammatory response to the tick bite. Mapping of sequence differences between OmCI and other tick lipocalins with different functions, combined with biochemical investigations of OmCI activity, supports the hypothesis that OmCI acts by preventing interaction with the C5 convertase, rather than by blocking the C5a cleavage site.


  • Organizational Affiliation

    Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, England, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
COMPLEMENT INHIBITOR150Ornithodoros moubataMutation(s): 2 
UniProt
Find proteins for Q5YD59 (Ornithodoros moubata)
Explore Q5YD59 
Go to UniProtKB:  Q5YD59
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5YD59
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Work: 0.169 
  • R-Value Observed: 0.169 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.17α = 90
b = 55.52β = 90
c = 60.62γ = 90
Software Package:
Software NamePurpose
TNTrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-05-01
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Other, Refinement description
  • Version 1.4: 2024-10-23
    Changes: Structure summary