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


View more in-depth experimental data

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