Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 97.74 kDa 
• Atom Count: 6506 
• Modelled Residue Count: 791 
• Deposited Residue Count: 836 
• Unique protein chains: 3

3O4O

Crystal structure of an Interleukin-1 receptor complex

• DOI: 10.2210/pdb3O4O/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3), Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2010-07-27 Released: 2010-09-01 
• Deposition Author(s): Wang, X.Q., Wang, D.L., Zhang, S.Y., Li, L., Liu, X., Mei, K.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 0.289 
• R-Value Work: 0.252 
• R-Value Observed: 0.253 

Literature

Structural insights into the assembly and activation of IL-1beta with its receptors

Wang, D.L., Zhang, S.Y., Li, L., Liu, X., Mei, K.R., Wang, X.Q.

(2010) Nat Immunol 11: 905-911

• PubMed: 20802483 
• DOI: 10.1038/ni.1925
• Primary Citation of Related Structures:  
  3O4O


• PubMed Abstract: 
  

Interleukin 1β (IL-1β) is a key orchestrator of inflammation and host defense that exerts its effects through IL-1 receptor type I (IL-1RI) and IL-1 receptor accessory protein (IL-1RAcP). How IL-1RAcP is recruited by IL-1β-IL-1RI to form the signaling-competent complex remains elusive. Here we present the crystal structure of IL-1β bound to IL-1 receptor type II (IL-1RII) and IL-1RAcP. IL-1β-IL-1RII generated a composite binding surface to recruit IL-1RAcP. Biochemical analysis demonstrated that IL-1β-IL-1RI and IL-1β-IL-1RII interacted similarly with IL-1RAcP. It also showed the importance of two loops of IL-1 receptor antagonist (IL-1Ra) in determining its antagonism. Our results provide a structural basis for assembly and activation of the IL-1 receptor and offer a general cytokine-receptor architecture that governs the IL-1 family of cytokines.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-1 beta	A	158	Homo sapiens	Mutation(s): 0  Gene Names: IL1B, IL1F2
UniProt & NIH Common Fund Data Resources
Find proteins for P01584 (Homo sapiens) Explore P01584  Go to UniProtKB:  P01584
PHAROS:  P01584 GTEx:  ENSG00000125538

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-1 receptor type 2	B [auth C]	339	Homo sapiens	Mutation(s): 0  Gene Names: IL1R2, IL1RB
UniProt & NIH Common Fund Data Resources
Find proteins for P27930 (Homo sapiens) Explore P27930  Go to UniProtKB:  P27930
PHAROS:  P27930 GTEx:  ENSG00000115590

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-1 receptor accessory protein	C [auth B]	339	Homo sapiens	Mutation(s): 0  Gene Names: IL1RAP, C3orf13, IL1R3 EC: 3.2.2.6
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NPH3 (Homo sapiens) Explore Q9NPH3  Go to UniProtKB:  Q9NPH3
PHAROS:  Q9NPH3 GTEx:  ENSG00000196083

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, E	2		N-Glycosylation

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	F [auth C], G [auth C], H [auth B], I [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 0.289 
• R-Value Work: 0.252 
• R-Value Observed: 0.253 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.83	α = 90
b = 177.47	β = 90
c = 180.66	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASES	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-07-27 
• Released Date: 2010-09-01 
Deposition Author(s): Wang, X.Q., Wang, D.L., Zhang, S.Y., Li, L., Liu, X., Mei, K.R.

Revision History  

• Version 1.0: 2010-09-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary