1MD6

High resolution crystal structure of murine IL-1F5 reveals unique loop conformation for specificity


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.204 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

High-Resolution Structure of Murine Interleukin 1 Homologue IL-1F5 Reveals Unique Loop Conformations for Receptor Binding Specificity.

Dunn, E.F.Gay, N.J.Bristow, A.F.Gearing, D.P.O'Neill, L.A.Pei, X.Y.

(2003) Biochemistry 42: 10938-10944

  • DOI: https://doi.org/10.1021/bi0341197
  • Primary Citation of Related Structures:  
    1MD6

  • PubMed Abstract: 

    Interleukin-1 (IL-1) F5 is a novel member of the IL-1 family. The IL-1 family are involved in innate immune responses to infection and injury. These cytokines bind to specific receptors and cause activation of NFkappaB and MAP kinase. IL-1F5 has a sequence identity of 44% to IL-1 receptor antagonist (IL-1Ra), a natural antagonist of the IL-1 system. Here we report the crystal structure of IL-1F5 to a resolution of 1.6 A. It has the same beta-trefoil fold as other IL-1 family members, and the hydrophobic core is well conserved. However, there are substantial differences in the loop conformations, structures that confer binding specificity for the cognate receptor to IL-1beta and the antagonist IL-1Ra. Docking and superimposition of the IL-1F5 structure suggest that is unlikely to bind to the interleukin1 receptor, consistent with biochemical studies. The structure IL-1F5 lacks features that confer antagonist properties on IL-1Ra, and we predict that like IL-1beta it will act as an agonist. These studies give insights into how distinct receptor specificities can evolve within related cytokine families.


  • Organizational Affiliation

    Department of Biochemistry, Trinity College, Dublin 2, Ireland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
interleukin 1 family, member 5 (delta)154Mus musculusMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9QYY1 (Mus musculus)
Explore Q9QYY1 
Go to UniProtKB:  Q9QYY1
IMPC:  MGI:1859325
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9QYY1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.204 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.932α = 90
b = 78.932β = 90
c = 69.74γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNSrefinement
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-09-30
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance