5VI4

IL-33/ST2/IL-1RAcP ternary complex structure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.215 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

IL-1 Family Cytokines Use Distinct Molecular Mechanisms to Signal through Their Shared Co-receptor.

Gunther, S.Deredge, D.Bowers, A.L.Luchini, A.Bonsor, D.A.Beadenkopf, R.Liotta, L.Wintrode, P.L.Sundberg, E.J.

(2017) Immunity 47: 510-523.e4

  • DOI: 10.1016/j.immuni.2017.08.004
  • Primary Citation of Related Structures:  
    5VI4

  • PubMed Abstract: 
  • Within the interleukin 1 (IL-1) cytokine family, IL-1 receptor accessory protein (IL-1RAcP) is the co-receptor for eight receptor-cytokine pairs, including those involving cytokines IL-1β and IL-33. Unlike IL-1β, IL-33 does not have a signaling complex that includes both its cognate receptor, ST2, and the shared co-receptor IL-1RAcP, which we now present here ...

    Within the interleukin 1 (IL-1) cytokine family, IL-1 receptor accessory protein (IL-1RAcP) is the co-receptor for eight receptor-cytokine pairs, including those involving cytokines IL-1β and IL-33. Unlike IL-1β, IL-33 does not have a signaling complex that includes both its cognate receptor, ST2, and the shared co-receptor IL-1RAcP, which we now present here. Although the IL-1β and IL-33 complexes shared structural features and engaged identical molecular surfaces of IL-1RAcP, these cytokines had starkly different strategies for co-receptor engagement and signal activation. Our data suggest that IL-1β binds to IL-1RI to properly present the cytokine to IL-1RAcP, whereas IL-33 binds to ST2 in order to conformationally constrain the cognate receptor in an IL-1RAcP-receptive state. These findings indicate that members of the IL-1 family of cytokines use distinct molecular mechanisms to signal through their shared co-receptor, and they provide the foundation from which to design new therapies to target IL-33 signaling.


    Organizational Affiliation

    Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD 21201, USA; Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA; Department of Microbiology & Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA. Electronic address: esundberg@ihv.umaryland.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Interleukin-33A, D158Mus musculusMutation(s): 4 
Gene Names: Il33
UniProt & NIH Common Fund Data Resources
Find proteins for Q8BVZ5 (Mus musculus)
Explore Q8BVZ5 
Go to UniProtKB:  Q8BVZ5
IMPC:  MGI:1924375
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Interleukin-1 receptor-like 1B, E309Mus musculusMutation(s): 0 
Gene Names: Il1rl1Ly84St2Ste2
EC: 3.2.2.6
UniProt
Find proteins for P14719 (Mus musculus)
Explore P14719 
Go to UniProtKB:  P14719
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Interleukin-1 receptor accessory proteinC, F339Mus musculusMutation(s): 4 
Gene Names: Il1rap
EC: 3.2.2.6
UniProt
Find proteins for Q61730 (Mus musculus)
Explore Q61730 
Go to UniProtKB:  Q61730
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
G [auth B], H [auth E], I [auth E]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: 2.79 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.215 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.314α = 90
b = 107.332β = 107.27
c = 176.036γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)United StatesR01AR068436
American Asthma FoundationUnited States13-0066

Revision History  (Full details and data files)

  • Version 1.0: 2017-09-27
    Type: Initial release
  • Version 1.1: 2019-12-11
    Changes: Author supporting evidence
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary