3O4O

Crystal structure of an Interleukin-1 receptor complex


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 

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This is version 2.0 of the entry. See complete history


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

  • 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 ...

    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.


    Organizational Affiliation

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



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Interleukin-1 betaA158Homo sapiensMutation(s): 0 
Gene Names: IL1BIL1F2
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Find proteins for P01584 (Homo sapiens)
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Go to UniProtKB:  P01584
PHAROS:  P01584
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Interleukin-1 receptor type 2B [auth C]339Homo sapiensMutation(s): 0 
Gene Names: IL1R2IL1RB
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Find proteins for P27930 (Homo sapiens)
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PHAROS:  P27930
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Interleukin-1 receptor accessory proteinC [auth B]339Homo sapiensMutation(s): 0 
Gene Names: IL1RAPC3orf13IL1R3
EC: 3.2.2.6
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Find proteins for Q9NPH3 (Homo sapiens)
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Go to UniProtKB:  Q9NPH3
PHAROS:  Q9NPH3
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  • Reference Sequence
Oligosaccharides

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Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseD, E2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
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 = 44.83α = 90
b = 177.47β = 90
c = 180.66γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
PHASESphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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