Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 106.06 kDa 
• Atom Count: 7078 
• Residue Count: 902 
• Unique protein chains: 4

3HMX

Crystal structure of ustekinumab FAB/IL-12 complex

• DOI: 10.2210/pdb3HMX/pdb

• Classification: Cytokine/IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


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

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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 

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

• PubMed: 20691190 
• 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 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.

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Organizational Affiliation: 

Centocor Research and Development, Inc., 145 King of Prussia Road, Radnor, PA 19087, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-12 subunit beta	A	306	Homo sapiens	Mutation(s): 0  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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-12 subunit alpha	B	197	Homo sapiens	Mutation(s): 0  Gene Names: IL12A, NKSF1
Find proteins for P29459 (Homo sapiens) Explore P29459  Go to UniProtKB:  P29459
NIH Common Fund Data Resources
PHAROS:  P29459 GTEx:  ENSG00000168811

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
USTEKINUMAB FAB LIGHT CHAIN	L	214	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
USTEKINUMAB FAB HEAVY CHAIN	H	226	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 5
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
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

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 = 55.092	α = 90
b = 116.435	β = 90
c = 182.781	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data processing
PHENIX	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
d*TREK	data reduction
d*TREK	data scaling
CNX	phasing

Structure Validation

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