5MJ4

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.255 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1038/ncomms6237
  • Primary Citation of Related Structures:  

  • 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- ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Interleukin-12 subunit beta
A
306Homo 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
179Homo 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
ALPHABODY MA12
C
118N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
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
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.255 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 57.850α = 90.00
b = 57.850β = 90.00
c = 366.480γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
XSCALEdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-01-11
    Type: Initial release
  • Version 1.1: 2017-02-01
    Type: Other