3B0W

Crystal structure of the orphan nuclear receptor ROR(gamma)t ligand-binding domain in complex with digoxin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural Basis of Digoxin That Antagonizes ROR{gamma}t Receptor Activity and Suppresses Th17 Cell Differentiation and Interleukin (IL)-17 Production

Fujita-Sato, S.Ito, S.Isobe, T.Ohyama, T.Wakabayashi, K.Morishita, K.Ando, O.Isono, F.

(2011) J Biol Chem 286: 31409-31417

  • DOI: 10.1074/jbc.M111.254003
  • Primary Citation of Related Structures:  
    3B0W

  • PubMed Abstract: 
  • The retinoic acid-related orphan nuclear receptor γt (RORγt)/RORγ2 is well known as a master regulator of interleukin 17 (IL-17)-producing helper T (Th17) cell development. To develop a therapeutic agent against Th17-mediated autoimmune diseases, we ...

    The retinoic acid-related orphan nuclear receptor γt (RORγt)/RORγ2 is well known as a master regulator of interleukin 17 (IL-17)-producing helper T (Th17) cell development. To develop a therapeutic agent against Th17-mediated autoimmune diseases, we screened chemical compounds and successfully found that digoxin inhibited IL-17 production. Further studies revealed that digoxin bound to the ligand binding domain of RORγt and suppressed Th17 differentiation without affecting Th1 differentiation. To better understand the structural basis for the inhibitory activity of digoxin, we determined the crystal structure of the RORγt ligand-binding domain in complex with digoxin at 2.2 Å resolution. The structure reveals that digoxin binds to the ligand-binding pocket protruding between helices H3 and H11 from the pocket. In addition, digoxin disrupts the key interaction important for the agonistic activity, resulting in preventing the positioning of helix H12 in the active conformation, thus antagonizing coactivator interaction. Functional studies demonstrated that digoxin inhibited RORγt activity and decreased IL-17 production but not RORα activity. Digoxin inhibited IL-17 production in CD4(+) T cells from experimental autoimmune encephalomyelitis mice. Our data indicates that RORγt is a promising therapeutic target for Th17-derived autoimmune diseases and our structural data will help to design novel RORγt antagonists.


    Organizational Affiliation

    Oncology Research Laboratories, R&D Division, Daiichi Sankyo Co., Ltd., Tokyo 134-8630, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear receptor ROR-gammaAB243Homo sapiensMutation(s): 0 
Gene Names: RORCNR1F3RORGRZRG
Find proteins for P51449 (Homo sapiens)
Explore P51449 
Go to UniProtKB:  P51449
NIH Common Fund Data Resources
PHAROS  P51449
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DGX
Query on DGX

Download CCD File 
A, B
DIGOXIN
C41 H64 O14
LTMHDMANZUZIPE-PUGKRICDSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DGXIC50 :  2000   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.716α = 90
b = 98.716β = 90
c = 129.176γ = 120
Software Package:
Software NamePurpose
SERGUIdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-07-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-09-28
    Changes: Database references, Structure summary
  • Version 1.3: 2017-10-11
    Changes: Refinement description