3HMW | pdb_00003hmw

Crystal structure of ustekinumab FAB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 
    0.287 (Depositor), 0.287 (DCC) 
  • R-Value Work: 
    0.228 (Depositor), 0.231 (DCC) 
  • R-Value Observed: 
    0.231 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

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 Biology 402: 797-812

  • DOI: https://doi.org/10.1016/j.jmb.2010.07.046
  • Primary Citation 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 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

Macromolecule Content 

  • Total Structure Weight: 48.06 kDa 
  • Atom Count: 3,426 
  • Modeled Residue Count: 432 
  • Deposited Residue Count: 440 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
USTEKINUMAB FAB LIGHT CHAINA [auth L]214Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
USTEKINUMAB FAB HEAVY CHAINB [auth H]226Homo sapiensMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free:  0.287 (Depositor), 0.287 (DCC) 
  • R-Value Work:  0.228 (Depositor), 0.231 (DCC) 
  • R-Value Observed: 0.231 (Depositor) 
Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 139.31α = 90
b = 139.31β = 90
c = 114.58γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
StructureStudiodata collection
d*TREKdata reduction
d*TREKdata scaling
CNXphasing

Structure Validation

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Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • 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 1.3: 2024-11-20
    Changes: Data collection, Database references, Derived calculations, Structure summary