4GRW

Structure of a complex of human IL-23 with 3 Nanobodies (Llama vHHs)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 

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This is version 2.0 of the entry. See complete history


Literature

Neutralization of Human Interleukin 23 by Multivalent Nanobodies Explained by the Structure of Cytokine-Nanobody Complex.

Desmyter, A.Spinelli, S.Boutton, C.Saunders, M.Blachetot, C.de Haard, H.Denecker, G.Van Roy, M.Cambillau, C.Rommelaere, H.

(2017) Front Immunol 8: 884-884

  • DOI: 10.3389/fimmu.2017.00884
  • Primary Citation of Related Structures:  
    4GRW

  • PubMed Abstract: 
  • The heterodimeric cytokine interleukin (IL) 23 comprises the IL12-shared p40 subunit and an IL23-specific subunit, p19. Together with IL12 and IL27, IL23 sits at the apex of the regulatory mechanisms shaping adaptive immune responses. IL23, together with IL17, plays an important role in the development of chronic inflammation and autoimmune inflammatory diseases ...

    The heterodimeric cytokine interleukin (IL) 23 comprises the IL12-shared p40 subunit and an IL23-specific subunit, p19. Together with IL12 and IL27, IL23 sits at the apex of the regulatory mechanisms shaping adaptive immune responses. IL23, together with IL17, plays an important role in the development of chronic inflammation and autoimmune inflammatory diseases. In this context, we generated monovalent antihuman IL23 variable heavy chain domain of llama heavy chain antibody (V HH ) domains (Nanobodies ® ) with low nanomolar affinity for human interleukin (hIL) 23. The crystal structure of a quaternary complex assembling hIL23 and several nanobodies against p19 and p40 subunits allowed identification of distinct epitopes and enabled rational design of a multivalent IL23-specific blocking nanobody. Taking advantage of the ease of nanobody formatting, multivalent IL23 nanobodies were assembled with properly designed linkers flanking an antihuman serum albumin nanobody, with improved hIL23 neutralization capacity in vitro and in vivo , as compared to the monovalent nanobodies. These constructs with long exposure time are excellent candidates for further developments targeting Crohn's disease, rheumatoid arthritis, and psoriasis.


    Organizational Affiliation

    Ablynx N.V., Ghent, Belgium.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Interleukin-23 subunit alpha AC189Homo sapiensMutation(s): 0 
Gene Names: IL23 p19IL23ASGRFUNQ2498/PRO5798
Find proteins for Q9NPF7 (Homo sapiens)
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Go to UniProtKB:  Q9NPF7
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PHAROS:  Q9NPF7
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Interleukin-12 subunit beta BD328Homo sapiensMutation(s): 0 
Gene Names: IL12 p40IL12BNKSF2
Find proteins for P29460 (Homo sapiens)
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Go to UniProtKB:  P29460
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PHAROS:  P29460
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Nanobody 124C4 EG125Lama glamaMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Nanobody 37D5 FJ126Lama glamaMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Nanobody 22E11 HI123Lama glamaMutation(s): 0 
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  • Reference Sequence
Oligosaccharides

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Entity ID: 6
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
K, L
5 N-Glycosylation Oligosaccharides Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.27α = 90
b = 135.14β = 90
c = 139.01γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
BUSTERrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-02-19
    Type: Initial release
  • Version 1.1: 2017-12-06
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary