1IRA

COMPLEX OF THE INTERLEUKIN-1 RECEPTOR WITH THE INTERLEUKIN-1 RECEPTOR ANTAGONIST (IL1RA)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.314 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

A new cytokine-receptor binding mode revealed by the crystal structure of the IL-1 receptor with an antagonist.

Schreuder, H.Tardif, C.Trump-Kallmeyer, S.Soffientini, A.Sarubbi, E.Akeson, A.Bowlin, T.Yanofsky, S.Barrett, R.W.

(1997) Nature 386: 194-200

  • DOI: 10.1038/386194a0

  • PubMed Abstract: 
  • Inflammation, regardless of whether it is provoked by infection or by tissue damage, starts with the activation of macrophages which initiate a cascade of inflammatory responses by producing the cytokines interleukin-1 (IL-1) and tumour necrosis fact ...

    Inflammation, regardless of whether it is provoked by infection or by tissue damage, starts with the activation of macrophages which initiate a cascade of inflammatory responses by producing the cytokines interleukin-1 (IL-1) and tumour necrosis factor-alpha (ref. 1). Three naturally occurring ligands for the IL-1 receptor (IL1R) exist: the agonists IL-1alpha and IL-1beta and the IL-1-receptor antagonist IL1RA (ref. 2). IL-1 is the only cytokine for which a naturally occurring antagonist is known. Here we describe the crystal structure at 2.7 A resolution of the soluble extracellular part of type-I IL1R complexed with IL1RA. The receptor consists of three immunoglobulin-like domains. Domains 1 and 2 are tightly linked, but domain three is completely separate and connected by a flexible linker. Residues of all three domains contact the antagonist and include the five critical IL1RA residues which were identified by site-directed mutagenesis. A region that is important for biological function in IL-1beta, the 'receptor trigger site' is not in direct contact with the receptor in the IL1RA complex. Modelling studies suggest that this IL-1beta trigger site might induce a movement of domain 3.


    Related Citations: 
    • Refined Crystal Structure of the Interleukin-1 Receptor Antagonist. Presence of a Disulfide Link and a Cis-Proline
      Schreuder, H.A.,Rondeau, J.M.,Tardif, C.,Soffientini, A.,Sarubbi, E.,Akeson, A.,Bowlin, T.L.,Yanofsky, S.,Barrett, R.W.
      (1995) Eur.J.Biochem. 227: 838
    • Crystals of Soluble Interleukin-1 Receptor Complexed with its Natural Antagonist Reveal a 1:1 Receptor-Ligand Complex
      Schreuder, H.,Tardif, C.,Soffientini, A.,Sarubbi, E.,Akeson, A.,Bowlin, T.,Yanofsky, S.,Barrett, R.W.
      (1995) FEBS Lett. 373: 39


    Organizational Affiliation

    Marion Merrell Dow Research Institute, Strasbourg, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
INTERLEUKIN-1 RECEPTOR ANTAGONIST
X
152Homo sapiensMutation(s): 0 
Gene Names: IL1RN (IL1F3, IL1RA)
Find proteins for P18510 (Homo sapiens)
Go to Gene View: IL1RN
Go to UniProtKB:  P18510
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
INTERLEUKIN-1 RECEPTOR
Y
319Homo sapiensMutation(s): 0 
Gene Names: IL1R1 (IL1R, IL1RA, IL1RT1)
Find proteins for P14778 (Homo sapiens)
Go to Gene View: IL1R1
Go to UniProtKB:  P14778
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download SDF File 
Download CCD File 
Y
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.314 
  • R-Value Work: 0.213 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 47.200α = 90.00
b = 84.600β = 90.00
c = 140.200γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
SQUASHphasing
XSCALEdata scaling
X-PLOR3.1phasing
XDSdata scaling
X-PLORmodel building
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-06-17
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2018-04-04
    Type: Data collection