5MZV

IL-23:IL-23R:Nb22E11 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural Activation of Pro-inflammatory Human Cytokine IL-23 by Cognate IL-23 Receptor Enables Recruitment of the Shared Receptor IL-12R beta 1.

Bloch, Y.Bouchareychas, L.Merceron, R.Skladanowska, K.Van den Bossche, L.Detry, S.Govindarajan, S.Elewaut, D.Haerynck, F.Dullaers, M.Adamopoulos, I.E.Savvides, S.N.

(2018) Immunity 48: 45-58.e6

  • DOI: 10.1016/j.immuni.2017.12.008
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Interleukin-23 (IL-23), an IL-12 family cytokine, plays pivotal roles in pro-inflammatory T helper 17 cell responses linked to autoimmune and inflammatory diseases. Despite intense therapeutic targeting, structural and mechanistic insights into recep ...

    Interleukin-23 (IL-23), an IL-12 family cytokine, plays pivotal roles in pro-inflammatory T helper 17 cell responses linked to autoimmune and inflammatory diseases. Despite intense therapeutic targeting, structural and mechanistic insights into receptor complexes mediated by IL-23, and by IL-12 family members in general, have remained elusive. We determined a crystal structure of human IL-23 in complex with its cognate receptor, IL-23R, and revealed that IL-23R bound to IL-23 exclusively via its N-terminal immunoglobulin domain. The structural and functional hotspot of this interaction partially restructured the helical IL-23p19 subunit of IL-23 and restrained its IL-12p40 subunit to cooperatively bind the shared receptor IL-12Rβ1 with high affinity. Together with structural insights from the interaction of IL-23 with the inhibitory antibody briakinumab and by leveraging additional IL-23:antibody complexes, we propose a mechanistic paradigm for IL-23 and IL-12 whereby cognate receptor binding to the helical cytokine subunits primes recruitment of the shared receptors via the IL-12p40 subunit.


    Organizational Affiliation

    Laboratory for Protein Biochemistry and Biomolecular Engineering, Department of Biochemistry and Microbiology, Ghent University, 9052 Ghent, Belgium; VIB-UGent Center for Inflammation Research, 9052 Ghent, Belgium.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Interleukin-12 subunit beta
A
328Homo sapiensMutation(s): 0 
Gene Names: IL12B (NKSF2)
Find proteins for P29460 (Homo sapiens)
Go to Gene View: IL12B
Go to UniProtKB:  P29460
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Interleukin-23 subunit alpha
B
198Homo sapiensMutation(s): 0 
Gene Names: IL23A (SGRF)
Find proteins for Q9NPF7 (Homo sapiens)
Go to Gene View: IL23A
Go to UniProtKB:  Q9NPF7
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Interleukin-23 receptor
C
330Homo sapiensMutation(s): 0 
Gene Names: IL23R
Find proteins for Q5VWK5 (Homo sapiens)
Go to Gene View: IL23R
Go to UniProtKB:  Q5VWK5
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Nanobody 22E11
D
156N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A, C
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MAN
Query on MAN

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Download CCD File 
A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA

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Download CCD File 
A, C
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
A, C
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.212 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 67.219α = 90.00
b = 112.190β = 106.24
c = 109.870γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
BUSTERrefinement
PHASERphasing
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
VLAIOBelgium--

Revision History 

  • Version 1.0: 2018-01-03
    Type: Initial release
  • Version 1.1: 2018-01-10
    Type: Database references
  • Version 1.2: 2018-01-31
    Type: Database references
  • Version 1.3: 2018-02-07
    Type: Structure summary