3L0L

Crystal structure of orphan nuclear receptor RORgamma in complex with natural ligand

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.189 

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Literature

Structural basis for hydroxycholesterols as natural ligands of orphan nuclear receptor RORgamma.

Jin, L., Martynowski, D., Zheng, S., Wada, T., Xie, W., Li, Y.

(2010) Mol Endocrinol 24: 923-929

  • DOI: 10.1210/me.2009-0507
  • Primary Citation of Related Structures:  
    3KYT, 3L0J, 3L0L

  • PubMed Abstract: 

    • The retinoic acid-related orphan receptor gamma (RORgamma) has important roles in development and metabolic homeostasis. Although the biological functions of RORgamma have been studied extensively, no ligands for RORgamma have been identified, and no structure of RORgamma has been reported ...

    The retinoic acid-related orphan receptor gamma (RORgamma) has important roles in development and metabolic homeostasis. Although the biological functions of RORgamma have been studied extensively, no ligands for RORgamma have been identified, and no structure of RORgamma has been reported. In this study, we showed that hydroxycholesterols promote the recruitment of coactivators by RORgamma using biochemical assays. We also report the crystal structures of the RORgamma ligand-binding domain bound with hydroxycholesterols. The structures reveal the binding modes of various hydroxycholesterols in the RORgamma pocket, with the receptors all adopting the canonical active conformation. Mutations that disrupt the binding of hydroxycholesterols abolish the constitutive activity of RORgamma. Our observations suggest an important role for the endogenous hydroxycholesterols in modulating RORgamma-dependent biological processes.

    Organizational Affiliation: 

    Key Laboratory for Cell Biology and Tumor Cell Engineering of the Ministry of Education, Xiamen University, Fujian 361005, China



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear receptor ROR-gammaA,
C [auth B]		248Homo sapiensMutation(s): 0 
Gene Names: RORC, NR1F3, RORG, RZRG
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
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
SCR2-2B [auth C],
D [auth E]		13Homo sapiensMutation(s): 0 
Gene Names: NCOA2, TIF2, BHLHE75, SRC2
UniProt & NIH Common Fund Data Resources
Find proteins for Q15596 (Homo sapiens)
Explore Q15596 
Go to UniProtKB:  Q15596
PHAROS:  Q15596
GTEx:  ENSG00000140396 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15596
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HC3
Query on HC3
Download Ideal Coordinates CCD File 
E [auth A],
F [auth B]		25-HYDROXYCHOLESTEROL
C27 H46 O2
INBGSXNNRGWLJU-ZHHJOTBYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
HC3 BindingDB:  3L0L EC50: 20 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.775α = 90
b = 86.262β = 90
c = 91.945γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-03-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2015-01-21
    Changes: Database references
  • Version 1.3: 2020-02-26
    Changes: Advisory, Derived calculations