5VB5

X-ray co-structure of nuclear receptor ROR-gammat Ligand Binding Domain with an inverse agonist and SRC2 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.226 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural studies unravel the active conformation of apo ROR gamma t nuclear receptor and a common inverse agonism of two diverse classes of ROR gamma t inhibitors.

Li, X.Anderson, M.Collin, D.Muegge, I.Wan, J.Brennan, D.Kugler, S.Terenzio, D.Kennedy, C.Lin, S.Labadia, M.E.Cook, B.Hughes, R.Farrow, N.A.

(2017) J. Biol. Chem. 292: 11618-11630

  • DOI: 10.1074/jbc.M117.789024
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The nuclear receptor retinoid acid receptor-related orphan receptor γt (RORγt) is a master regulator of the Th17/IL-17 pathway that plays crucial roles in the pathogenesis of autoimmunity. RORγt has recently emerged as a highly promising target for t ...

    The nuclear receptor retinoid acid receptor-related orphan receptor γt (RORγt) is a master regulator of the Th17/IL-17 pathway that plays crucial roles in the pathogenesis of autoimmunity. RORγt has recently emerged as a highly promising target for treatment of a number of autoimmune diseases. Through high-throughput screening, we previously identified several classes of inverse agonists for RORγt. Here, we report the crystal structures for the ligand-binding domain of RORγt in both apo and ligand-bound states. We show that apo RORγt adopts an active conformation capable of recruiting coactivator peptides and present a detailed analysis of the structural determinants that stabilize helix 12 (H12) of RORγt in the active state in the absence of a ligand. The structures of ligand-bound RORγt reveal that binding of the inverse agonists disrupts critical interactions that stabilize H12. This destabilizing effect is supported by ab initio calculations and experimentally by a normalized crystallographic B-factor analysis. Of note, the H12 destabilization in the active state shifts the conformational equilibrium of RORγt toward an inactive state, which underlies the molecular mechanism of action for the inverse agonists reported here. Our findings highlight that nuclear receptor structure and function are dictated by a dynamic conformational equilibrium and that subtle changes in ligand structures can shift this equilibrium in opposite directions, leading to a functional switch from agonists to inverse agonists.


    Organizational Affiliation

    From the Departments of Small Molecule Discovery Research and xiang.li@boehringer-ingelheim.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nuclear receptor ROR-gamma, SRC2 chimera
A
280Homo sapiensMutation(s): 0 
Gene Names: RORC (NR1F3, RORG, RZRG), NCOA2 (BHLHE75, SRC2, TIF2)
Find proteins for P51449 (Homo sapiens)
Go to Gene View: RORC
Go to UniProtKB:  P51449
Find proteins for Q15596 (Homo sapiens)
Go to Gene View: NCOA2
Go to UniProtKB:  Q15596
Small Molecules
Ligands 2 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
92A
Query on 92A

Download SDF File 
Download CCD File 
A
N-[(2R)-3-(4-{[3-(4-chlorophenyl)propanoyl]amino}phenyl)-1-(4-methylpiperidin-1-yl)-1-oxopropan-2-yl]-4-methylpentanamide
C30 H40 Cl N3 O3
LEQKKFVJROREDY-HHHXNRCGSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
92AKd: 350 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.226 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.193 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 60.468α = 90.00
b = 60.468β = 90.00
c = 154.997γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXphasing
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-03-28 
  • Released Date: 2017-06-07 
  • Deposition Author(s): Li, X.

Revision History 

  • Version 1.0: 2017-06-07
    Type: Initial release
  • Version 1.1: 2017-07-26
    Type: Database references