4KC3

Cytokine/receptor binary complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2702 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.238 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural insights into the interaction of IL-33 with its receptors.

Liu, X.Hammel, M.He, Y.Tainer, J.A.Jeng, U.S.Zhang, L.Wang, S.Wang, X.

(2013) Proc.Natl.Acad.Sci.USA 110: 14918-14923

  • DOI: 10.1073/pnas.1308651110

  • PubMed Abstract: 
  • Interleukin (IL)-33 is an important member of the IL-1 family that has pleiotropic activities in innate and adaptive immune responses in host defense and disease. It signals through its ligand-binding primary receptor ST2 and IL-1 receptor accessory ...

    Interleukin (IL)-33 is an important member of the IL-1 family that has pleiotropic activities in innate and adaptive immune responses in host defense and disease. It signals through its ligand-binding primary receptor ST2 and IL-1 receptor accessory protein (IL-1RAcP), both of which are members of the IL-1 receptor family. To clarify the interaction of IL-33 with its receptors, we determined the crystal structure of IL-33 in complex with the ectodomain of ST2 at a resolution of 3.27 Å. Coupled with structure-based mutagenesis and binding assay, the structural results define the molecular mechanism by which ST2 specifically recognizes IL-33. Structural comparison with other ligand-receptor complexes in the IL-1 family indicates that surface-charge complementarity is critical in determining ligand-binding specificity of IL-1 primary receptors. Combined crystallography and small-angle X-ray-scattering studies reveal that ST2 possesses hinge flexibility between the D3 domain and D1D2 module, whereas IL-1RAcP exhibits a rigid conformation in the unbound state in solution. The molecular flexibility of ST2 provides structural insights into domain-level conformational change of IL-1 primary receptors upon ligand binding, and the rigidity of IL-1RAcP explains its inability to bind ligands directly. The solution architecture of IL-33-ST2-IL-1RAcP complex from small-angle X-ray-scattering analysis resembles IL-1β-IL-1RII-IL-1RAcP and IL-1β-IL-1RI-IL-1RAcP crystal structures. The collective results confer IL-33 structure-function relationships, supporting and extending a general model for ligand-receptor assembly and activation in the IL-1 family.


    Organizational Affiliation

    Ministry of Education Key Laboratory of Protein Science, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Interleukin-33
A
159Homo sapiensMutation(s): 0 
Gene Names: IL33 (C9orf26, IL1F11, NFHEV)
Find proteins for O95760 (Homo sapiens)
Go to Gene View: IL33
Go to UniProtKB:  O95760
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Interleukin-1 receptor-like 1
B
309Homo sapiensMutation(s): 0 
Gene Names: IL1RL1 (DER4, ST2, T1)
Find proteins for Q01638 (Homo sapiens)
Go to Gene View: IL1RL1
Go to UniProtKB:  Q01638
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download SDF File 
Download CCD File 
B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2702 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.238 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 329.924α = 90.00
b = 329.924β = 90.00
c = 43.731γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHENIXrefinement
PHASERphasing
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-04-24 
  • Released Date: 2013-08-28 
  • Deposition Author(s): Liu, X., Wang, X.Q.

Revision History 

  • Version 1.0: 2013-08-28
    Type: Initial release
  • Version 1.1: 2013-09-11
    Type: Database references
  • Version 1.2: 2013-09-25
    Type: Database references