9VZQ | pdb_00009vzq

Crystal structure of RORgamma in complex with novel inverse agonist


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 
    0.251 (Depositor), 0.253 (DCC) 
  • R-Value Work: 
    0.202 (Depositor), 0.209 (DCC) 
  • R-Value Observed: 
    0.204 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Structural basis for diosgenin as an inverse agonist of retinoic acid receptor-related orphan receptor gamma.

Chen, S.Tian, S.Liang, J.Wang, R.Li, Y.

(2026) Sci Rep 16: 4765-4765

  • DOI: https://doi.org/10.1038/s41598-026-35006-6
  • Primary Citation Related Structures: 
    9VZQ

  • PubMed Abstract: 

    Retinoic acid receptor-related orphan receptor γ (RORγ) is a member of the nuclear receptor superfamily involved in many physiological activities such as metabolic and autoimmune diseases, and therefore a potential therapeutic drug target. Here we report that the steroidal sapogenin, diosgenin, a novel ligand for RORγ, inhibits the transcriptional activity of the RORγ with distinctive properties in coregulator recruitment. Biochemical and cell-based studies indicated that diosgenin functions as a selective RORγ inverse agonist by inducing both coactivator and corepressor binding to RORγ, thereby uncovering a molecular mechanism for the actions of this natural compound. Further, the crystal structure of diosgenin complexed with the ligand-binding domain of RORγ reveals a unique binding mode including the active conformation of AF-2 helix and the conformational shift of Helix 11. Structural and functional studies suggest the plasticity of RORγ pockets in recognizing ligands and the vital roles of the backbone of diosgenin in recognizing RORγ. Our results provide a unique inverse agonist template of RORγ with high selectivity and efficacy, which contributes to further drug design and optimization targeting RORγ.


  • Organizational Affiliation
    • The State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Fujian, 361005, China.

Macromolecule Content 

  • Total Structure Weight: 30.55 kDa 
  • Atom Count: 2,198 
  • Modeled Residue Count: 253 
  • Deposited Residue Count: 259 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Nuclear receptor ROR-gamma246Homo 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
GTEx:  ENSG00000143365 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP51449
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Nuclear receptor coactivator 113Homo sapiensMutation(s): 0 
Gene Names: NCOA1BHLHE74SRC1
EC: 2.3.1.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q15788 (Homo sapiens)
Explore Q15788 
Go to UniProtKB:  Q15788
PHAROS:  Q15788
GTEx:  ENSG00000084676 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15788
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
YUV
(Subject of Investigation/LOI)

Query on YUV



Download:Ideal Coordinates CCD File
C [auth A](25R)-14beta,17beta-spirost-5-en-3beta-ol
C27 H42 O3
WQLVFSAGQJTQCK-VKROHFNGSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free:  0.251 (Depositor), 0.253 (DCC) 
  • R-Value Work:  0.202 (Depositor), 0.209 (DCC) 
  • R-Value Observed: 0.204 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.644α = 90
b = 61.644β = 90
c = 155.618γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2026-06-03
    Type: Initial release