8CR5 | pdb_00008cr5

Murine Interleukin-12 receptor beta 1 domain 1 in complex with murine Interleukin-12 beta.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 
    0.282 (Depositor), 0.283 (DCC) 
  • R-Value Work: 
    0.241 (Depositor), 0.242 (DCC) 
  • R-Value Observed: 
    0.243 (Depositor) 

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 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: 69.96 kDa 
  • Atom Count: 3,363 
  • Modeled Residue Count: 406 
  • Deposited Residue Count: 609 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Interleukin-12 subunit beta344Mus musculusMutation(s): 1 
Gene Names: Il12b
UniProt & NIH Common Fund Data Resources
Find proteins for P43432 (Mus musculus)
Explore P43432 
Go to UniProtKB:  P43432
IMPC:  MGI:96540
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43432
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P43432-1
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Interleukin-12 receptor subunit beta-1265Mus musculusMutation(s): 0 
Gene Names: Il12rb1Il12rb
UniProt & NIH Common Fund Data Resources
Find proteins for Q60837 (Mus musculus)
Explore Q60837 
Go to UniProtKB:  Q60837
IMPC:  MGI:104579
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ60837
Glycosylation
Glycosylation Sites: 1Go to GlyGen: Q60837-1
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
4N-Glycosylation
Glycosylation Resources
GlyTouCan: G81315DD
GlyCosmos: G81315DD
GlyGen: G81315DD

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
D [auth B]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free:  0.282 (Depositor), 0.283 (DCC) 
  • R-Value Work:  0.241 (Depositor), 0.242 (DCC) 
  • R-Value Observed: 0.243 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 29.22α = 90
b = 165.09β = 90.435
c = 51.87γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata 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)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: 2024-10-09
    Changes: Structure summary