3NJ5

Crystal structure of chicken IL-1 hydrophobic cavity mutant 157


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural and functional comparison of cytokine interleukin-1 beta from chicken and human

Cheng, C.S.Chen, W.T.Lee, L.H.Chen, Y.W.Chang, S.Y.Lyu, P.C.Yin, H.S.

(2011) Mol.Immunol. 48: 947-955

  • DOI: 10.1016/j.molimm.2011.01.002
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Interleukin-1 beta (IL-1β) is an important cytokine in the immune system. The properties of avian IL-1βs are less well understood than the mammalian IL-1βs, and there is no available structure of avian IL-1βs in the Protein Data Bank. Here, we report ...

    Interleukin-1 beta (IL-1β) is an important cytokine in the immune system. The properties of avian IL-1βs are less well understood than the mammalian IL-1βs, and there is no available structure of avian IL-1βs in the Protein Data Bank. Here, we report the crystal structures of wild-type and Y157F mutant IL-1βs from chicken. Both the wild-type and mutant IL-1βs share a beta-trefoil conformation similar to that of human IL-1β and also have an internal hydrophobic cavity. However, the cavity sizes clearly differ from that of human IL-1β due to the packing of hydrophobic residues. Our studies also reveal that the relative thermal stability of IL-1βs does not correlate with cavity size but rather is dependent on the amino acid residues present around the cavity. This cavity serves as a scaffold for maintaining the structure of the IL-1β core region but does not have a biological function per se. Moreover, we found that human IL-1β cannot induce chemokine expression in chicken fibroblasts or elevate plasma cortisol levels in chickens, implying a lack of cross-species bioactivity. Close examination reveals that significant structural and sequence differences occur in the terminal and some loop regions between human and chicken IL-1βs. These variable regions have been shown to be critical for receptor binding, thus resulting in a lack of species cross-reactivity between human and chicken IL-1β.


    Organizational Affiliation

    Institute of Bioinformatics and Structural Biology, and College of Life Sciences, National Tsing Hua University, Hsinchu 300, Taiwan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
IL-1 beta
A
162Gallus gallusMutation(s): 1 
Gene Names: il-1beta (IL1B, IL1beta)
Find proteins for O73909 (Gallus gallus)
Go to UniProtKB:  O73909
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.178 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 35.800α = 90.00
b = 38.666β = 90.00
c = 103.334γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
MOLREPphasing
HKL-2000data reduction
REFMACrefinement
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2010-06-17 
  • Released Date: 2011-06-22 
  • Deposition Author(s): Yin, H.S., Chen, Y.W.

Revision History 

  • Version 1.0: 2011-06-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-08
    Type: Refinement description