5VI4 | pdb_00005vi4

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 
    0.267 (Depositor), 0.270 (DCC) 
  • R-Value Work: 
    0.212 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 
    0.215 (Depositor) 

Starting Models: experimental
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This is version 1.4 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: https://doi.org/10.1016/j.immuni.2017.08.004
  • Primary Citation 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. 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.

Macromolecule Content 

  • Total Structure Weight: 185.66 kDa 
  • Atom Count: 11,304 
  • Modeled Residue Count: 1,405 
  • Deposited Residue Count: 1,612 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Interleukin-33
A, D
158Mus 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
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8BVZ5
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Interleukin-1 receptor-like 1
B, E
309Mus musculusMutation(s): 0 
Gene Names: Il1rl1Ly84St2Ste2
EC: 3.2.2.6
UniProt
Find proteins for P14719 (Mus musculus)
Explore P14719 
Go to UniProtKB:  P14719
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14719
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P14719-1
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Interleukin-1 receptor accessory protein
C, F
339Mus musculusMutation(s): 4 
Gene Names: Il1rap
EC: 3.2.2.6
UniProt
Find proteins for Q61730 (Mus musculus)
Explore Q61730 
Go to UniProtKB:  Q61730
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ61730
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free:  0.267 (Depositor), 0.270 (DCC) 
  • R-Value Work:  0.212 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 0.215 (Depositor) 
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
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.4: 2024-10-16
    Changes: Structure summary