8C7M

Interleukin 12 receptor subunit beta-1 Fn domains in complex with antagonistic FAb fragment.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.56 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.204 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structures of complete extracellular receptor assemblies mediated by IL-12 and IL-23.

Bloch, Y.Felix, J.Merceron, R.Provost, M.Symakani, R.A.De Backer, R.Lambert, E.Mehdipour, A.R.Savvides, S.N.

(2024) Nat Struct Mol Biol 31: 591-597

  • DOI: https://doi.org/10.1038/s41594-023-01190-6
  • Primary Citation of Related Structures:  
    8C7M, 8CR5, 8CR6, 8CR8, 8ODX, 8ODZ, 8OE0, 8OE4, 8PB1, 8PPM

  • PubMed Abstract: 

    Cell-surface receptor complexes mediated by pro-inflammatory interleukin (IL)-12 and IL-23, both validated therapeutic targets, are incompletely understood due to the lack of structural insights into their complete extracellular assemblies. Furthermore, there is a paucity of structural details describing the IL-12-receptor interaction interfaces, in contrast to IL-23-receptor complexes. Here we report structures of fully assembled mouse IL-12/human IL-23-receptor complexes comprising the complete extracellular segments of the cognate receptors determined by electron cryo-microscopy. The structures reveal key commonalities but also surprisingly diverse features. Most notably, whereas IL-12 and IL-23 both utilize a conspicuously presented aromatic residue on their α-subunit as a hotspot to interact with the N-terminal Ig domain of their high-affinity receptors, only IL-12 juxtaposes receptor domains proximal to the cell membrane. Collectively, our findings will help to complete our understanding of cytokine-mediated assemblies of tall cytokine receptors and will enable a cytokine-specific interrogation of IL-12/IL-23 signaling in physiology and disease.


  • Organizational Affiliation

    Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Interleukin-12 receptor subunit beta-1
A, B
313Homo sapiensMutation(s): 0 
Gene Names: IL12RB1IL12RIL12RB
UniProt & NIH Common Fund Data Resources
Find proteins for P42701 (Homo sapiens)
Explore P42701 
Go to UniProtKB:  P42701
GTEx:  ENSG00000096996 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP42701
Glycosylation
Glycosylation Sites: 4Go to GlyGen: P42701-1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
FAb4 Heavy chainC,
E [auth H]
231Homo sapiens x Mus musculus hybrid cell lineMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
FAb4 Crystal Kappa Light chainD,
F [auth L]
212Homo sapiens x Mus musculus hybrid cell lineMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.56 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.204 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.663α = 90
b = 140.178β = 90
c = 219.363γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Research Foundation - Flanders (FWO)BelgiumG0B4918N
Research Foundation - Flanders (FWO)Belgium12S0519N

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-31
    Type: Initial release
  • Version 1.1: 2024-02-07
    Changes: Database references
  • Version 1.2: 2024-05-01
    Changes: Database references