6NWT

RORgamma Ligand Binding Domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

HDX-MS reveals structural determinants for ROR gamma hyperactivation by synthetic agonists.

Strutzenberg, T.S.Garcia-Ordonez, R.D.Novick, S.J.Park, H.Chang, M.R.Doebellin, C.He, Y.Patouret, R.Kamenecka, T.M.Griffin, P.R.

(2019) Elife 8

  • DOI: 10.7554/eLife.47172
  • Primary Citation of Related Structures:  
    6NWT, 6NWS, 6NWU

  • PubMed Abstract: 
  • Members of the nuclear receptor (NR) superfamily regulate both physiological and pathophysiological processes ranging from development and metabolism to inflammation and cancer. Synthetic small molecules targeting NRs are often deployed as therapeutics to correct aberrant NR signaling or as chemical probes to explore the role of the receptor in physiology ...

    Members of the nuclear receptor (NR) superfamily regulate both physiological and pathophysiological processes ranging from development and metabolism to inflammation and cancer. Synthetic small molecules targeting NRs are often deployed as therapeutics to correct aberrant NR signaling or as chemical probes to explore the role of the receptor in physiology. Nearly half of NRs do not have specific cognate ligands (termed orphan NRs) and it's unclear if they possess ligand dependent activities. Here we demonstrate that ligand-dependent action of the orphan RORγ can be defined by selectively disrupting putative endogenous-but not synthetic-ligand binding. Furthermore, the characterization of a library of RORγ modulators reveals that structural dynamics of the receptor assessed by HDX-MS correlate with activity in biochemical and cell-based assays. These findings, corroborated with X-ray co-crystallography and site-directed mutagenesis, collectively reveal the structural determinants of RORγ activation, which is critical for designing RORγ agonists for cancer immunotherapy.


    Organizational Affiliation

    Department of Molecular Medicine, The Scripps Research Institute, Jupiter, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear receptor ROR-gammaA, B [auth C]245Homo sapiensMutation(s): 0 
Gene Names: RORCNR1F3RORGRZRG
UniProt & NIH Common Fund Data Resources
Find proteins for P51449 (Homo sapiens)
Explore P51449 
Go to UniProtKB:  P51449
PHAROS:  P51449
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
L7P
Query on L7P

Download Ideal Coordinates CCD File 
C [auth A], D [auth C]1,1,1,3,3,3-hexafluoro-2-[2-fluoro-4'-({4-[(pyridin-4-yl)methyl]piperazin-1-yl}methyl)[1,1'-biphenyl]-4-yl]propan-2-ol
C26 H24 F7 N3 O
KVHKWAZUPPBMLL-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.59α = 90
b = 99.59β = 90
c = 129.6γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
pointlessdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01CA206493
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesF31GM126842

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-10
    Type: Initial release
  • Version 1.1: 2019-12-04
    Changes: Author supporting evidence