5MJ4

INTERLEUKIN-23 COMPLEX WITH AN ANTAGONISTIC ALPHABODY, CRYSTAL FORM 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.258 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 2.2 of the entry. See complete history


Literature

STRUCTURAL BASIS OF IL-23 ANTAGONISM BY AN ALPHABODY PROTEIN

Desmet, J.Verstraete, K.Bloch, Y.Lorent, E.Wen, Y.Devreese, B.Vandenbroucke, K.Loverix, S.Hettmann, T.Deroo, S.Somers, K.Henderikx, P.Lasters, I.Savvides, S.

(2014) Nature Communications 5: 5237

  • DOI: https://doi.org/10.1038/ncomms6237
  • Primary Citation of Related Structures:  
    5MJ3, 5MJ4

  • PubMed Abstract: 

    Protein scaffolds can provide a promising alternative to antibodies for various biomedical and biotechnological applications, including therapeutics. Here we describe the design and development of the Alphabody, a protein scaffold featuring a single-chain antiparallel triple-helix coiled-coil fold. We report affinity-matured Alphabodies with favourable physicochemical properties that can specifically neutralize human interleukin (IL)-23, a pivotal therapeutic target in autoimmune inflammatory diseases such as psoriasis and multiple sclerosis. The crystal structure of human IL-23 in complex with an affinity-matured Alphabody reveals how the variable interhelical groove of the scaffold uniquely targets a large epitope on the p19 subunit of IL-23 to harness fully the hydrophobic and hydrogen-bonding potential of tryptophan and tyrosine residues contributed by p19 and the Alphabody, respectively. Thus, Alphabodies are suitable for targeting protein-protein interfaces of therapeutic importance and can be tailored to interrogate desired design and binding-mode principles via efficient selection and affinity-maturation strategies.


  • Organizational Affiliation

    1] COMPLIX N.V., Technology Park 4, 9052 Ghent, Belgium [2].


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Interleukin-12 subunit beta306Homo sapiensMutation(s): 0 
Gene Names: IL12BNKSF2
UniProt & NIH Common Fund Data Resources
Find proteins for P29460 (Homo sapiens)
Explore P29460 
Go to UniProtKB:  P29460
PHAROS:  P29460
GTEx:  ENSG00000113302 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29460
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P29460-1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Interleukin-23 subunit alpha179Homo sapiensMutation(s): 0 
Gene Names: IL23ASGRFUNQ2498/PRO5798
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NPF7 (Homo sapiens)
Explore Q9NPF7 
Go to UniProtKB:  Q9NPF7
PHAROS:  Q9NPF7
GTEx:  ENSG00000110944 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NPF7
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ALPHABODY MA12118synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChains 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
D
5N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO
GlyCosmos:  G22768VO
GlyGen:  G22768VO
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.258 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.85α = 90
b = 57.85β = 90
c = 366.48γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-11
    Type: Initial release
  • Version 1.1: 2017-02-01
    Changes: Other
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 2.2: 2024-10-23
    Changes: Structure summary