3HMX

Crystal structure of ustekinumab FAB/IL-12 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.215 

wwPDB Validation   3D Report Full Report



Literature

Structural basis for the dual recognition of IL-12 and IL-23 by ustekinumab.

Luo, J.Wu, S.J.Lacy, E.R.Orlovsky, Y.Baker, A.Teplyakov, A.Obmolova, G.Heavner, G.A.Richter, H.T.Benson, J.

(2010) J Mol Biol 402: 797-812

  • DOI: 10.1016/j.jmb.2010.07.046
  • Primary Citation of Related Structures:  
    3HMW, 3HMX

  • PubMed Abstract: 
  • Interleukin (IL)-12 and IL-23 are heterodimeric proinflammatory cytokines that share a common p40 subunit, paired with p35 and p19 subunits, respectively. They represent an attractive class of therapeutic targets for the treatment of psoriasis and other ...

    Interleukin (IL)-12 and IL-23 are heterodimeric proinflammatory cytokines that share a common p40 subunit, paired with p35 and p19 subunits, respectively. They represent an attractive class of therapeutic targets for the treatment of psoriasis and other immune-mediated diseases. Ustekinumab is a fully human monoclonal antibody (mAb) that binds specifically to IL-12/IL-23p40 and neutralizes human IL-12 and IL-23 bioactivity. The crystal structure of ustekinumab Fab (antigen binding fragment of mAb), in complex with human IL-12, has been determined by X-ray crystallography at 3.0 Å resolution. Ustekinumab Fab binds the D1 domain of the p40 subunit in a 1:1 ratio in the crystal, consistent with a 2 cytokines:1 mAb stoichiometry, as measured by isothermal titration calorimetry. The structure indicates that ustekinumab binds to the same epitope on p40 in both IL-12 and IL-23 with identical interactions. Mutational analyses confirm that several residues identified in the IL-12/IL-23p40 epitope provide important molecular binding interactions with ustekinumab. The electrostatic complementarity between the mAb antigen binding site and the p40 D1 domain epitope appears to play a key role in antibody/antigen recognition specificity. Interestingly, this structure also reveals significant structural differences in the p35 subunit and p35/p40 interface, compared with the published crystal structure of human IL-12, suggesting unusual and potentially functionally relevant structural flexibility of p35, as well as p40/p35 recognition. Collectively, these data describe unique observations about IL-12p35 and ustekinumab interactions with p40 that account for its dual binding and neutralization of IL-12 and IL-23.


    Organizational Affiliation

    Centocor Research and Development, Inc., 145 King of Prussia Road, Radnor, PA 19087, USA. jluo@its.jnj.com



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Interleukin-12 subunit beta A306Homo sapiensMutation(s): 0 
Gene Names: IL12BNKSF2
Find proteins for P29460 (Homo sapiens)
Explore P29460 
Go to UniProtKB:  P29460
NIH Common Fund Data Resources
PHAROS:  P29460
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Interleukin-12 subunit alpha B197Homo sapiensMutation(s): 0 
Gene Names: IL12ANKSF1
Find proteins for P29459 (Homo sapiens)
Explore P29459 
Go to UniProtKB:  P29459
NIH Common Fund Data Resources
PHAROS:  P29459
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
USTEKINUMAB FAB LIGHT CHAIN L214Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
USTEKINUMAB FAB HEAVY CHAIN H226Homo sapiensMutation(s): 0 
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  • Reference Sequence
Oligosaccharides

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Entity ID: 5
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
5 N-Glycosylation Oligosaccharides Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.215 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.092α = 90
b = 116.435β = 90
c = 182.781γ = 90
Software Package:
Software NamePurpose
d*TREKdata processing
PHENIXrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
d*TREKdata reduction
d*TREKdata scaling
CNXphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2009-05-29 
  • Released Date: 2010-06-09 
  • Deposition Author(s): Luo, J.

Revision History 

  • Version 1.0: 2010-06-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2015-07-22
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary