3D87

Crystal structure of Interleukin-23

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.323 
  • R-Value Work: 0.268 
  • R-Value Observed: 0.269 

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This is version 1.2 of the entry. See complete history. 


Literature

Crystal structures of the pro-inflammatory cytokine interleukin-23 and its complex with a high-affinity neutralizing antibody

Beyer, B.M., Ingram, R., Ramanathan, L., Reichert, P., Le, H.V., Madison, V., Orth, P.

(2008) J Mol Biol 382: 942-955

  • DOI: 10.1016/j.jmb.2008.08.001
  • Primary Citation of Related Structures:  
    3D87, 3D85

  • PubMed Abstract: 

    • Interleukin (IL)-23 is a pro-inflammatory cytokine playing a key role in the pathogenesis of several autoimmune and inflammatory diseases. We have determined the crystal structures of the heterodimeric p19-p40 IL-23 and its complex with the Fab (antigen-binding fragment) of a neutralizing antibody at 2 ...

    Interleukin (IL)-23 is a pro-inflammatory cytokine playing a key role in the pathogenesis of several autoimmune and inflammatory diseases. We have determined the crystal structures of the heterodimeric p19-p40 IL-23 and its complex with the Fab (antigen-binding fragment) of a neutralizing antibody at 2.9 and 1.9 A, respectively. The IL-23 structure closely resembles that of IL-12. They share the common p40 subunit, and IL-23 p19 overlaps well with IL-12 p35. Along the hydrophilic heterodimeric interface, fewer charged residues are involved for IL-23 compared with IL-12. The binding site of the Fab is located exclusively on the p19 subunit, and comparison with published cytokine-receptor structures suggests that it overlaps with the IL-23 receptor binding site.

    Organizational Affiliation: 

    Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Interleukin-23 subunit p19 A, C178Homo sapiensMutation(s): 0 
Gene Names: IL23A, SGRF, UNQ2498/PRO5798
Find proteins for Q9NPF7 (Homo sapiens)
Explore Q9NPF7 
Go to UniProtKB:  Q9NPF7
NIH Common Fund Data Resources
PHAROS:  Q9NPF7
GTEx:  ENSG00000110944
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Interleukin-12 subunit p40 B, D306Homo sapiensMutation(s): 1 
Gene Names: IL12B, NKSF2
Find proteins for P29460 (Homo sapiens)
Explore P29460 
Go to UniProtKB:  P29460
NIH Common Fund Data Resources
PHAROS:  P29460
GTEx:  ENSG00000113302
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN
Download Ideal Coordinates CCD File 
D
alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N		 Ligand Interaction
PO4
Query on PO4
Download Ideal Coordinates CCD File 
B, D
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K		 Ligand Interaction
K
Query on K
Download Ideal Coordinates CCD File 
B, D
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.323 
  • R-Value Work: 0.268 
  • R-Value Observed: 0.269 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.098α = 90
b = 240.587β = 90
c = 141.781γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
AMoREphasing
BUSTER-TNTrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-09-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary