1UHL

Crystal structure of the LXRalfa-RXRbeta LBD heterodimer

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.326 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.224 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Crystal structure of the heterodimeric complex of LXRalpha and RXRbeta ligand-binding domains in a fully agonistic conformation

Svensson, S., Ostberg, T., Jacobsson, M., Norstrom, C., Stefansson, K., Hallen, D., Johansson, I.C., Zachrisson, K., Ogg, D., Jendeberg, L.

(2003) EMBO J 22: 4625-4633

  • DOI: 10.1093/emboj/cdg456
  • Primary Citation of Related Structures:  
    1UHL

  • PubMed Abstract: 

    • The nuclear receptor heterodimers of liver X receptor (LXR) and retinoid X receptor (RXR) are key transcriptional regulators of genes involved in lipid homeostasis and inflammation. We report the crystal structure of the ligand-binding domains (LBDs) of LXRalpha and RXRbeta complexed to the synthetic LXR agonist T-0901317 and the RXR agonist methoprene acid (Protein Data Base entry 1UHL) ...

    The nuclear receptor heterodimers of liver X receptor (LXR) and retinoid X receptor (RXR) are key transcriptional regulators of genes involved in lipid homeostasis and inflammation. We report the crystal structure of the ligand-binding domains (LBDs) of LXRalpha and RXRbeta complexed to the synthetic LXR agonist T-0901317 and the RXR agonist methoprene acid (Protein Data Base entry 1UHL). Both LBDs are in agonist conformation with GRIP-1 peptides bound at the coactivator binding sites. T-0901317 occupies the center of the LXR ligand-binding pocket and its hydroxyl head group interacts with H421 and W443, residues identified by mutational analysis as critical for ligand-induced transcriptional activation by T-0901317 and various endogenous oxysterols. The topography of the pocket suggests a common anchoring of these oxysterols via their 22-, 24- or 27-hydroxyl group to H421 and W443. Polyunsaturated fatty acids act as LXR antagonists and an E267A mutation was found to enhance their transcriptional inhibition. The present structure provides a powerful tool for the design of novel modulators that can be used to characterize further the physiological functions of the LXR-RXR heterodimer.

    Organizational Affiliation: 

    Department of Structural Chemistry, Biovitrum AB, Lindhagensgatan 133, SE-112 76 Stockholm, Sweden. stefan.j.svensson@biovitrum.com



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Retinoic acid receptor RXR-beta A236Homo sapiensMutation(s): 0 
Gene Names: RXRB, NR2B2
Find proteins for P28702 (Homo sapiens)
Explore P28702 
Go to UniProtKB:  P28702
NIH Common Fund Data Resources
PHAROS:  P28702
GTEx:  ENSG00000204231
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Oxysterols receptor LXR-alpha B242Homo sapiensMutation(s): 0 
Gene Names: NR1H3, LXRA
Find proteins for Q13133 (Homo sapiens)
Explore Q13133 
Go to UniProtKB:  Q13133
NIH Common Fund Data Resources
PHAROS:  Q13133
GTEx:  ENSG00000025434
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
10-mer peptide from Nuclear receptor coactivator 2 C, D10N/AMutation(s): 0 
Find proteins for Q15596 (Homo sapiens)
Explore Q15596 
Go to UniProtKB:  Q15596
NIH Common Fund Data Resources
PHAROS:  Q15596
GTEx:  ENSG00000140396
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
444
Query on 444
Download Ideal Coordinates CCD File 
B
N-(2,2,2-TRIFLUOROETHYL)-N-{4-[2,2,2-TRIFLUORO-1-HYDROXY-1-(TRIFLUOROMETHYL)ETHYL]PHENYL}BENZENESULFONAMIDE
C17 H12 F9 N O3 S
SGIWFELWJPNFDH-UHFFFAOYSA-N		 Ligand Interaction
MEI
Query on MEI
Download Ideal Coordinates CCD File 
A
(2E,4E)-11-METHOXY-3,7,11-TRIMETHYLDODECA-2,4-DIENOIC ACID
C16 H28 O3
MNYBEULOKRVZKY-ATCPXPEISA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
444Kd:  92   nM  BindingDB
444IC50:  14000   nM  BindingDB
444EC50:  210   nM  BindingDB
444EC50:  170   nM  BindingDB
444EC50:  10   nM  BindingDB
444EC50:  190   nM  BindingDB
444IC50:  75   nM  BindingDB
444EC50:  290   nM  BindingDB
444EC50:  250   nM  BindingDB
444IC50:  100   nM  BindingDB
444IC50:  26000   nM  BindingDB
444EC50:  400   nM  BindingDB
444EC50:  340   nM  BindingDB
444EC50:  20   nM  BindingDB
444IC50:  9   nM  BindingDB
444EC50:  370   nM  BindingDB
444EC50:  373   nM  BindingDB
444EC50:  359   nM  BindingDB
444IC50:  10   nM  BindingDB
444EC50:  28   nM  BindingDB
444IC50:  13   nM  BindingDB
444EC50:  500   nM  BindingDB
444EC50:  30   nM  BindingDB
444EC50:  490   nM  BindingDB
444EC50:  55   nM  BindingDB
444Ki:  24   nM  BindingDB
444EC50:  40   nM  BindingDB
444EC50:  940   nM  BindingDB
444EC50:  63   nM  BindingDB
444EC50:  60   nM  BindingDB
444EC50:  6   nM  BindingDB
444IC50:  30   nM  BindingDB
444EC50:  85   nM  BindingDB
444EC50:  91   nM  BindingDB
444EC50:  1430   nM  BindingDB
444EC50:  135   nM  BindingDB
444EC50:  140   nM  BindingDB
444EC50:  3.200000047683716   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.326 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.224 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.634α = 90
b = 88.996β = 90
c = 90.795γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-06-01
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-05-23
    Changes: Data collection