3U3U

Crystal structure of the tablysin-15-leukotriene E4 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tablysin 15A [auth C]233Tabanus yaoMutation(s): 0 
UniProt
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
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.774α = 90
b = 69.774β = 90
c = 85.473γ = 120
Software Package:
Software NamePurpose
d*TREKdata scaling
d*TREKdata reduction
PHENIXrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
PHASERphasing

Structure Validation

View Full Validation Report



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: 2015-01-28
    Changes: Other
  • Version 1.4: 2024-10-16
    Changes: Data collection, Database references, Derived calculations, Structure summary