Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 54.77 kDa 
• Atom Count: 3780 
• Modelled Residue Count: 456 
• Deposited Residue Count: 471 
• Unique protein chains: 2

1IRA

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

• DOI: 10.2210/pdb1IRA/pdb

• Classification: COMPLEX (CYTOKINE RECEPTOR/ANTAGONIST)
• Organism(s): Homo sapiens
• Expression System: Escherichia coli, Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 1998-04-09 Released: 1998-06-17 
• Deposition Author(s): Schreuder, H.A., Tardif, C., Tramp-Kalmeyer, S., Soffientini, A., Sarubbi, E., Akeson, A., Bowlin, T., Yanofsky, S., Barrett, R.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.314 
• R-Value Work: 0.213 
• R-Value Observed: 0.213 

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

• PubMed: 9062194 
• DOI: 10.1038/386194a0
• Primary Citation of Related Structures:  
  1IRA


• 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 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.

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Related Citations: 

• 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

• 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

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Organizational Affiliation: 

Marion Merrell Dow Research Institute, Strasbourg, France.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
INTERLEUKIN-1 RECEPTOR ANTAGONIST	X	152	Homo sapiens	Mutation(s): 0  Gene Names: IL1RN, IL1F3, IL1RA
Find proteins for P18510 (Homo sapiens) Explore P18510  Go to UniProtKB:  P18510
NIH Common Fund Data Resources
PHAROS:  P18510 GTEx:  ENSG00000136689

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
INTERLEUKIN-1 RECEPTOR	Y	319	Homo sapiens	Mutation(s): 0  Gene Names: IL1R1, IL1R, IL1RA, IL1RT1 EC: 3.2.2.6
Find proteins for P14778 (Homo sapiens) Explore P14778  Go to UniProtKB:  P14778
NIH Common Fund Data Resources
PHAROS:  P14778 GTEx:  ENSG00000115594

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	Y	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.314 
• R-Value Work: 0.213 
• R-Value Observed: 0.213 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.2	α = 90
b = 84.6	β = 90
c = 140.2	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
XSCALE	data scaling
SQUASH	phasing
X-PLOR	model building
X-PLOR	refinement
XDS	data reduction
X-PLOR3.1	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1998-04-09 
• Released Date: 1998-06-17 
Deposition Author(s): Schreuder, H.A., Tardif, C., Tramp-Kalmeyer, S., Soffientini, A., Sarubbi, E., Akeson, A., Bowlin, T., Yanofsky, S., Barrett, R.W.

Revision History  

• Version 1.0: 1998-06-17
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2018-04-04
  Changes: Data collection
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary