8PPM | pdb_00008ppm

IL-12Rb1 neutralizing Fab4, crystal kappa variant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 
    0.220 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.193 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 
    0.195 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8PPM

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 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.

Macromolecule Content 

  • Total Structure Weight: 48.1 kDa 
  • Atom Count: 3,475 
  • Modeled Residue Count: 431 
  • Deposited Residue Count: 443 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Fab4 heavy chainA [auth H]231Homo sapiens x Mus musculus hybrid cell lineMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Fab4 Light chain, crystal kappa variantB [auth L]212Homo sapiens x Mus musculus hybrid cell lineMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free:  0.220 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.193 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 0.195 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.069α = 90
b = 72.069β = 90
c = 163.833γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-07
    Type: Initial release
  • Version 1.1: 2024-05-01
    Changes: Database references
  • Version 1.2: 2024-11-13
    Changes: Structure summary