3NJ5 | pdb_00003nj5

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 (Depositor), 0.234 (DCC) 
  • R-Value Work: 
    0.178 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 
    0.181 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3NJ5

This is version 1.3 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: https://doi.org/10.1016/j.molimm.2011.01.002
  • Primary Citation Related Structures: 
    2WRY, 3NJ5

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 18.06 kDa 
  • Atom Count: 1,309 
  • Modeled Residue Count: 152 
  • Deposited Residue Count: 162 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
IL-1 beta162Gallus gallusMutation(s): 1 
UniProt
Find proteins for O73909 (Gallus gallus)
Explore O73909 
Go to UniProtKB:  O73909
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO73909
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free:  0.237 (Depositor), 0.234 (DCC) 
  • R-Value Work:  0.178 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 0.181 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.8α = 90
b = 38.666β = 90
c = 103.334γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-06-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-08
    Changes: Refinement description
  • Version 1.3: 2024-03-20
    Changes: Data collection, Database references