8DPS

The structure of the interleukin 11 signalling complex, truncated gp130


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.47 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structures of the interleukin 11 signalling complex reveal gp130 dynamics and the inhibitory mechanism of a cytokine variant.

Metcalfe, R.D.Hanssen, E.Fung, K.Y.Aizel, K.Kosasih, C.C.Zlatic, C.O.Doughty, L.Morton, C.J.Leis, A.P.Parker, M.W.Gooley, P.R.Putoczki, T.L.Griffin, M.D.W.

(2023) Nat Commun 14: 7543-7543

  • DOI: https://doi.org/10.1038/s41467-023-42754-w
  • Primary Citation of Related Structures:  
    8DPS, 8DPT, 8DPU, 8DPV, 8DPW

  • PubMed Abstract: 

    Interleukin (IL-)11, an IL-6 family cytokine, has pivotal roles in autoimmune diseases, fibrotic complications, and solid cancers. Despite intense therapeutic targeting efforts, structural understanding of IL-11 signalling and mechanistic insights into current inhibitors are lacking. Here we present cryo-EM and crystal structures of the human IL-11 signalling complex, including the complex containing the complete extracellular domains of the shared IL-6 family β-receptor, gp130. We show that complex formation requires conformational reorganisation of IL-11 and that the membrane-proximal domains of gp130 are dynamic. We demonstrate that the cytokine mutant, IL-11 Mutein, competitively inhibits signalling in human cell lines. Structural shifts in IL-11 Mutein underlie inhibition by altering cytokine binding interactions at all three receptor-engaging sites and abrogating the final gp130 binding step. Our results reveal the structural basis of IL-11 signalling, define the molecular mechanisms of an inhibitor, and advance understanding of gp130-containing receptor complexes, with potential applications in therapeutic development.


  • Organizational Affiliation

    Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, 3010, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Interleukin-6 receptor subunit beta
A, D
303Homo sapiensMutation(s): 0 
Gene Names: IL6ST
UniProt & NIH Common Fund Data Resources
Find proteins for P40189 (Homo sapiens)
Explore P40189 
Go to UniProtKB:  P40189
PHAROS:  P40189
GTEx:  ENSG00000134352 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40189
Glycosylation
Glycosylation Sites: 3Go to GlyGen: P40189-1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Interleukin-11
B, E
169Homo sapiensMutation(s): 0 
Gene Names: IL11
UniProt & NIH Common Fund Data Resources
Find proteins for P20809 (Homo sapiens)
Explore P20809 
Go to UniProtKB:  P20809
PHAROS:  P20809
GTEx:  ENSG00000095752 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20809
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Interleukin-11 receptor subunit alpha
C, F
298Homo sapiensMutation(s): 1 
Gene Names: IL11RA
UniProt & NIH Common Fund Data Resources
Find proteins for Q14626 (Homo sapiens)
Explore Q14626 
Go to UniProtKB:  Q14626
PHAROS:  Q14626
GTEx:  ENSG00000137070 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14626
Glycosylation
Glycosylation Sites: 1Go to GlyGen: Q14626-1
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
G, I
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
H, J
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.47 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)AustraliaAPP1147621

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-29
    Type: Initial release
  • Version 1.1: 2024-05-01
    Changes: Database references
  • Version 1.2: 2024-10-30
    Changes: Data collection, Structure summary