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 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 2.3 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: https://doi.org/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. 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

    Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Centre National de la Recherche Scientifique (CNRS), Marseille, France.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Interleukin-23 subunit alpha
A, C
189Homo sapiensMutation(s): 0 
Gene Names: IL23 p19IL23ASGRFUNQ2498/PRO5798
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NPF7 (Homo sapiens)
Explore Q9NPF7 
Go to UniProtKB:  Q9NPF7
PHAROS:  Q9NPF7
GTEx:  ENSG00000110944 
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UniProt GroupQ9NPF7
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Interleukin-12 subunit beta
B, D
328Homo sapiensMutation(s): 0 
Gene Names: IL12 p40IL12BNKSF2
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: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Nanobody 124C4
E, G
125Lama glamaMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Nanobody 37D5
F, J
126Lama glamaMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Nanobody 22E11
H, I
123Lama glamaMutation(s): 0 
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  • Reference Sequence
Oligosaccharides

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Entity ID: 6
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
K, L
5N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO
GlyCosmos:  G22768VO
GlyGen:  G22768VO
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
  • Version 2.1: 2023-09-13
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 2.2: 2023-12-27
    Changes: Advisory, Derived calculations
  • Version 2.3: 2024-10-30
    Changes: Structure summary