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 8TLD | pdb_00008tld

Structure of the IL-5 Signaling Complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history. 

Literature

Structure of the interleukin-5 receptor complex exemplifies the organizing principle of common beta cytokine signaling.

Caveney, N.A., Rodriguez, G.E., Pollmann, C., Meyer, T., Borowska, M.T., Wilson, S.C., Wang, N., Xiang, X., Householder, K.D., Tao, P., Su, L.L., Saxton, R.A., Piehler, J., Garcia, K.C.

(2024) Mol Cell 84: 1995-2005.e7

  • DOI: https://doi.org/10.1016/j.molcel.2024.03.023
  • Primary Citation Related Structures: 
    8TLD

  • PubMed Abstract: 

    Cytokines regulate immune responses by binding to cell surface receptors, including the common subunit beta (βc), which mediates signaling for GM-CSF, IL-3, and IL-5. Despite known roles in inflammation, the structural basis of IL-5 receptor activation remains unclear. We present the cryo-EM structure of the human IL-5 ternary receptor complex, revealing architectural principles for IL-5, GM-CSF, and IL-3. In mammalian cell culture, single-molecule imaging confirms hexameric IL-5 complex formation on cell surfaces. Engineered chimeric receptors show that IL-5 signaling, as well as IL-3 and GM-CSF, can occur through receptor heterodimerization, obviating the need for higher-order assemblies of βc dimers. These findings provide insights into IL-5 and βc receptor family signaling mechanisms, aiding in the development of therapies for diseases involving deranged βc signaling.


  • Organizational Affiliation: 
    • Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Centre for Blood Research, University of British Columbia, Vancouver, BC, Canada. Electronic address: nathanael.caveney@ubc.ca.

Macromolecule Content 

  • Total Structure Weight: 241.53 kDa 
  • Atom Count: 5,982 
  • Modeled Residue Count: 731 
  • Deposited Residue Count: 2,118 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytokine receptor common subunit betaA [auth B],
D [auth E]
717Homo sapiensMutation(s): 0 
Gene Names: CSF2RB, IL3RB, IL5RB
UniProt & NIH Common Fund Data Resources
Find proteins for P32927 (Homo sapiens)
Explore P32927 
Go to UniProtKB:  P32927
PHAROS:  P32927
GTEx:  ENSG00000100368 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32927
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Interleukin-5B [auth C],
C [auth D]
146Homo sapiensMutation(s): 0 
Gene Names: IL5
UniProt & NIH Common Fund Data Resources
Find proteins for P05113 (Homo sapiens)
Explore P05113 
Go to UniProtKB:  P05113
PHAROS:  P05113
GTEx:  ENSG00000113525 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05113
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P05113-1
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Interleukin-5 receptor subunit alphaE [auth F]392Homo sapiensMutation(s): 0 
Gene Names: IL5RA
UniProt & NIH Common Fund Data Resources
Find proteins for Q01344 (Homo sapiens)
Explore Q01344 
Go to UniProtKB:  Q01344
PHAROS:  Q01344
GTEx:  ENSG00000091181 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ01344
Glycosylation
Glycosylation Sites: 4Go to GlyGen: Q01344-1
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC4

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-10
    Type: Initial release
  • Version 1.1: 2024-11-20
    Changes: Data collection, Structure summary
  • Version 1.2: 2024-12-11
    Changes: Data collection, Database references
  • Version 1.3: 2025-05-28
    Changes: Data collection