4S15

Crystal structure of the orphan nuclear receptor RORalpha ligand-binding domain in complex with 4alpha-caboxyl, 4beta-methyl-zymosterol (4ACD8)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.897 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Identification of Natural ROR gamma Ligands that Regulate the Development of Lymphoid Cells.

Santori, F.R.Huang, P.van de Pavert, S.A.Douglass, E.F.Leaver, D.J.Haubrich, B.A.Keber, R.Lorbek, G.Konijn, T.Rosales, B.N.Rozman, D.Horvat, S.Rahier, A.Mebius, R.E.Rastinejad, F.Nes, W.D.Littman, D.R.

(2015) Cell Metab 21: 286-297

  • DOI: 10.1016/j.cmet.2015.01.004
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Mice deficient in the nuclear hormone receptor RORγt have defective development of thymocytes, lymphoid organs, Th17 cells, and type 3 innate lymphoid cells. RORγt binds to oxysterols derived from cholesterol catabolism, but it is not clear whether t ...

    Mice deficient in the nuclear hormone receptor RORγt have defective development of thymocytes, lymphoid organs, Th17 cells, and type 3 innate lymphoid cells. RORγt binds to oxysterols derived from cholesterol catabolism, but it is not clear whether these are its natural ligands. Here, we show that sterol lipids are necessary and sufficient to drive RORγt-dependent transcription. We combined overexpression, RNAi, and genetic deletion of metabolic enzymes to study RORγ-dependent transcription. Our results are consistent with the RORγt ligand(s) being a cholesterol biosynthetic intermediate (CBI) downstream of lanosterol and upstream of zymosterol. Analysis of lipids bound to RORγ identified molecules with molecular weights consistent with CBIs. Furthermore, CBIs stabilized the RORγ ligand-binding domain and induced coactivator recruitment. Genetic deletion of metabolic enzymes upstream of the RORγt-ligand(s) affected the development of lymph nodes and Th17 cells. Our data suggest that CBIs play a role in lymphocyte development potentially through regulation of RORγt.


    Organizational Affiliation

    The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY 10016, USA. Electronic address: fsantof01@gmail.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nuclear receptor ROR-alpha
A, B
256Homo sapiensMutation(s): 0 
Gene Names: RORA (NR1F1, RZRA)
Find proteins for P35398 (Homo sapiens)
Go to Gene View: RORA
Go to UniProtKB:  P35398
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nuclear receptor-interacting protein 1
C, D
12Homo sapiensMutation(s): 0 
Gene Names: NRIP1
Find proteins for P48552 (Homo sapiens)
Go to Gene View: NRIP1
Go to UniProtKB:  P48552
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
4D8
Query on 4D8

Download SDF File 
Download CCD File 
A, B
(3beta,4alpha,5beta,14beta)-3-hydroxy-4-methylcholesta-8,24-diene-4-carboxylic acid
4alpha-carboxy-4beta-methyl-zymosterol
C29 H46 O3
MYWAIWDQTCHPTH-LJAIZBFVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.897 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.174 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 71.194α = 90.00
b = 80.305β = 90.00
c = 113.104γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
HKL-3000data reduction
HKL-3000data scaling
HKL-3000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-02-11
    Type: Initial release
  • Version 1.1: 2015-02-25
    Type: Database references