Crystal structure of the selenomethionine derivative of tablysin-15

Experimental Data Snapshot

  • Resolution: 1.57 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 

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Structure of protein having inhibitory disintegrin and leukotriene scavenging functions contained in single domain.

Xu, X.Francischetti, I.M.Lai, R.Ribeiro, J.M.Andersen, J.F.

(2012) J Biol Chem 287: 10967-10976

  • DOI: https://doi.org/10.1074/jbc.M112.340471
  • Primary Citation of Related Structures:  
    3U3L, 3U3N, 3U3U

  • PubMed Abstract: 

    The antihemostatic/antiangiogenic protein tablysin-15 is a member of the CAP (cysteine-rich secretory, antigen 5, and pathogenesis-related 1 protein) superfamily and has been shown to bind the integrins α(IIb)β(3) and α(V)β(3) by means of an Arg-Gly-Asp (RGD) tripeptide sequence. Here we describe the x-ray crystal structure of tablysin-15 and show that the RGD motif is located in a novel structural context. The motif itself is contained in a type II β-turn structure that is similar in its conformation to the RGD sequence of the cyclic pentapeptide cilengitide when bound to integrin α(V)β(3). The CAP domain also contains a hydrophobic channel that appears to bind a fatty acid molecule in the crystal structure after purification from Escherichia coli. After delipidation of the protein, tablysin-15 was found to bind proinflammatory cysteinyl leukotrienes with submicromolar affinities. The structure of the leukotriene E(4)-tablysin-15 complex shows that the ligand binds with the nonfunctionalized end of the fatty acid chain buried in the hydrophobic pocket, whereas the carboxylate end of the ligand binds forms hydrogen bond/salt bridge interactions with polar side chains at the channel entrance. Therefore, tablysin-15 functions as an inhibitor of integrin function and as an anti-inflammatory scavenger of eicosanoids.

  • Organizational Affiliation

    Laboratory of Malaria and Vector Research, NIAID, National Intitutes of Health, Bethesda, Maryland 20892, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tablysin 15A [auth C]233Tabanus yaoMutation(s): 0 
Find proteins for F8QQG5 (Tabanus yao)
Explore F8QQG5 
Go to UniProtKB:  F8QQG5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF8QQG5
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
Experimental Data & Validation

Experimental Data

  • Resolution: 1.57 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.556α = 90
b = 69.556β = 90
c = 86.209γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
SHELXEmodel building

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-02-15
    Type: Initial release
  • Version 1.1: 2012-05-23
    Changes: Database references
  • Version 1.2: 2012-10-17
    Changes: Database references
  • Version 1.3: 2017-11-08
    Changes: Refinement description