1P8D

X-Ray Crystal Structure of LXR Ligand Binding Domain with 24(S),25-epoxycholesterol

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.214 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history. 


Literature

X-ray crystal structure of the liver X receptor beta ligand binding domain: regulation by a histidine-tryptophan switch.

Williams, S., Bledsoe, R.K., Collins, J.L., Boggs, S., Lambert, M.H., Miller, A.B., Moore, J., McKee, D.D., Moore, L., Nichols, J., Parks, D., Watson, M., Wisely, B., Willson, T.M.

(2003) J Biol Chem 278: 27138-27143

  • DOI: 10.1074/jbc.M302260200
  • Primary Citation of Related Structures:  
    1P8D

  • PubMed Abstract: 

    • The x-ray crystal structures of the human liver X receptor beta ligand binding domain complexed to sterol and nonsterol agonists revealed a perpendicular histidinetryptophan switch that holds the receptor in its active conformation. Hydrogen bonding interactions with the ligand act to position the His-435 imidazole ring against the Trp-457 indole ring, allowing an electrostatic interaction that holds the AF2 helix in the active position ...

    The x-ray crystal structures of the human liver X receptor beta ligand binding domain complexed to sterol and nonsterol agonists revealed a perpendicular histidinetryptophan switch that holds the receptor in its active conformation. Hydrogen bonding interactions with the ligand act to position the His-435 imidazole ring against the Trp-457 indole ring, allowing an electrostatic interaction that holds the AF2 helix in the active position. The neutral oxysterol 24(S),25-epoxycholesterol accepts a hydrogen bond from His-435 that positions the imidazole ring of the histidine above the pyrrole ring of the tryptophan. In contrast, the acidic T0901317 hydroxyl group makes a shorter hydrogen bond with His-435 that pulls the imidazole over the electron-rich benzene ring of the tryptophan, possibly strengthening the electrostatic interaction. Point mutagenesis of Trp-457 supports the observation that the ligand-histidine-tryptophan coupling is different between the two ligands. The lipophilic liver X receptor ligand-binding pocket is larger than the corresponding steroid hormone receptors, which allows T0901317 to adopt two distinct conformations. These results provide a molecular basis for liver X receptor activation by a wide range of endogenous neutral and acidic ligands.

    Organizational Affiliation: 

    GlaxoSmithKline, Discovery Research, Research Triangle Park, NC 27709, USA. shawn.p.williams@gsk.com



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Oxysterols receptor LXR-beta A, B250Homo sapiensMutation(s): 0 
Gene Names: NR1H2 OR LXRB OR UNR OR NER, NR1H2, LXRB, NER, UNR
Find proteins for P55055 (Homo sapiens)
Explore P55055 
Go to UniProtKB:  P55055
NIH Common Fund Data Resources
PHAROS:  P55055
GTEx:  ENSG00000131408
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
nuclear receptor coactivator 1 isoform 3 C, D25N/AMutation(s): 0 
Find proteins for Q15788 (Homo sapiens)
Explore Q15788 
Go to UniProtKB:  Q15788
NIH Common Fund Data Resources
PHAROS:  Q15788
GTEx:  ENSG00000084676
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CO1
Query on CO1
Download Ideal Coordinates CCD File 
A, B
17-[3-(3,3-DIMETHYL-OXIRANYL)-1-METHYL-PROPYL]-10,13-DIMETHYL-2,3,4,7,8,9,10,11,12,13,14,15,16,17-TETRADECAHYDRO-1H-CYC LOPENTA[A]PHENANTHREN-3-OL
C27 H44 O2
OSENKJZWYQXHBN-XVYZBDJZSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
CO1EC50:  168   nM  BindingDB
CO1EC50:  286   nM  BindingDB
CO1EC50:  20000   nM  BindingDB
CO1EC50:  400   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.214 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.166α = 90
b = 120.012β = 90
c = 147.56γ = 90
Software Package:
Software NamePurpose
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-07-08
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2011-11-16
    Changes: Atomic model
  • Version 1.4: 2017-10-11
    Changes: Refinement description