5X8S

Crystal Structure of the mutant Human ROR gamma Ligand Binding Domain With Ursolic acid.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.179 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Ternary complex of human ROR gamma ligand-binding domain, inverse agonist and SMRT peptide shows a unique mechanism of corepressor recruitment

Noguchi, M.Nomura, A.Murase, K.Doi, S.Yamaguchi, K.Hirata, K.Shiozaki, M.Hirashima, S.Kotoku, M.Yamaguchi, T.Katsuda, Y.Steensma, R.Li, X.Tao, H.Tse, B.Fenn, M.Babine, R.Bradley, E.Crowe, P.Thacher, S.Adachi, T.Kamada, M.

(2017) Genes Cells 22: 535-551

  • DOI: https://doi.org/10.1111/gtc.12494
  • Primary Citation of Related Structures:  
    5X8Q, 5X8S, 5X8U, 5X8W, 5X8X

  • PubMed Abstract: 

    Retinoid-related orphan receptor gamma (RORγ) directly controls the differentiation of Th17 cell and the production of interleukin-17, which plays an integral role in autoimmune diseases. To obtain insight into RORγ, we have determined the first crystal structure of a ternary complex containing RORγ ligand-binding domain (LBD) bound with a novel synthetic inhibitor and a repressor peptide, 22-mer peptide from silencing mediator of retinoic acid and thyroid hormone receptor (SMRT). Comparison of a binary complex of nonliganded (apo) RORγ-LBD with a nuclear receptor co-activator (NCoA-1) peptide has shown that our inhibitor displays a unique mechanism different from those caused by natural inhibitor, ursolic acid (UA). The compound unprecedentedly induces indirect disruption of a hydrogen bond between His479 on helix 11 (H11) and Tyr502 on H12, which is crucial for active conformation. This crystallographic study will allow us to develop novel synthetic compounds for autoimmune disease therapy.


  • Organizational Affiliation

    Pharmaceutical Frontier Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-13-2, Fukuura, Kanazawa-Ku, Yokohama, Kanagawa, 236-0004, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear receptor ROR-gamma
A, B
258Homo sapiensMutation(s): 0 
Gene Names: RORCNR1F3RORGRZRG
UniProt
Find proteins for G1RH57 (Nomascus leucogenys)
Explore G1RH57 
Go to UniProtKB:  G1RH57
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG1RH57
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
6Q5 BindingDB:  5X8S IC50: min: 130, max: 9410 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.179 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.95α = 90
b = 116.95β = 90
c = 77.96γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-07
    Type: Initial release
  • Version 1.1: 2017-06-28
    Changes: Database references
  • Version 1.2: 2020-06-17
    Changes: Database references, Source and taxonomy, Structure summary
  • Version 1.3: 2023-11-22
    Changes: Data collection, Database references, Refinement description