5X8Q

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1111/gtc.12494
  • Structures With Same Primary Citation

  • 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 crys ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nuclear receptor ROR-gamma
A, C, E, G
258Homo sapiensMutation(s): 2 
Gene Names: RORCNR1F3RORGRZRG
Find proteins for P51449 (Homo sapiens)
Go to UniProtKB:  P51449
NIH Common Fund Data Resources
PHAROS  P51449
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nuclear receptor corepressor 2
B, D, F, H
22Homo sapiensMutation(s): 0 
Gene Names: NCOR2CTG26
Find proteins for Q9Y618 (Homo sapiens)
Go to UniProtKB:  Q9Y618
NIH Common Fund Data Resources
PHAROS  Q9Y618
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
82R
Query on 82R

Download CCD File 
A, C, E, G
(1R,2S,4S,5'R,6R,7S,8R,9S,10R,12S,13S,16S,18S)-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icosane-6,2'-oxane]-10,16-diol
C27 H44 O4
BQNMOLSYHYSCMS-TUUYSWIFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.63α = 90
b = 71.94β = 90.06
c = 99.21γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-06-07
    Type: Initial release
  • Version 1.1: 2017-06-28
    Changes: Database references