4NQA

Crystal structure of liganded hRXR-alpha/hLXR-beta heterodimer on DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.102 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of the retinoid X receptor alpha-liver X receptor beta (RXR alpha-LXR beta ) heterodimer on DNA.

Lou, X.Toresson, G.Benod, C.Suh, J.H.Philips, K.J.Webb, P.Gustafsson, J.A.

(2014) Nat.Struct.Mol.Biol. 21: 277-281

  • DOI: 10.1038/nsmb.2778

  • PubMed Abstract: 
  • Nuclear receptors (NRs) are conditional transcription factors with common multidomain organization that bind diverse DNA elements. How DNA sequences influence NR conformation is poorly understood. Here we report the crystal structure of the human ret ...

    Nuclear receptors (NRs) are conditional transcription factors with common multidomain organization that bind diverse DNA elements. How DNA sequences influence NR conformation is poorly understood. Here we report the crystal structure of the human retinoid X receptor α-liver X receptor β (RXRα-LXRβ) heterodimer on its cognate element, an AGGTCA direct repeat spaced by 4 nt. The complex has an extended X-shaped arrangement, with DNA- and ligand-binding domains crossed, in contrast to the parallel domain arrangement of other NRs that bind an AGGTCA direct repeat spaced by 1 nt. The LXRβ core binds DNA via canonical contacts and auxiliary DNA contacts that enhance affinity for the response element. Comparisons of RXRα-LXRβs in the crystal asymmetric unit and with previous NR structures reveal flexibility in NR organization and suggest a role for RXRα in adaptation of heterodimeric complexes to DNA.


    Organizational Affiliation

    1] Center for Nuclear Receptors and Cell Signaling, University of Houston, Houston, Texas, USA. [2] Genomic Medicine Program, Houston Methodist Research Institute, Houston, Texas, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Retinoic acid receptor RXR-alpha
A, H
365Homo sapiensMutation(s): 0 
Gene Names: RXRA (NR2B1)
Find proteins for P19793 (Homo sapiens)
Go to Gene View: RXRA
Go to UniProtKB:  P19793
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Liver X nuclear receptor beta
B, I
391Homo sapiensMutation(s): 0 
Gene Names: NR1H2 (LXRB, NER, UNR)
Find proteins for P55055 (Homo sapiens)
Go to Gene View: NR1H2
Go to UniProtKB:  P55055
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Nuclear receptor coactivator 2
C, D, J, K
13Homo sapiensMutation(s): 0 
Gene Names: NCOA2 (BHLHE75, SRC2, TIF2)
Find proteins for Q15596 (Homo sapiens)
Go to Gene View: NCOA2
Go to UniProtKB:  Q15596
Entity ID: 4
MoleculeChainsLengthOrganism
5'-D(*TP*AP*AP*GP*GP*TP*CP*AP*CP*TP*TP*CP*AP*GP*GP*TP*CP*A)-3'E,L18synthetic construct
Entity ID: 5
MoleculeChainsLengthOrganism
5'-D(*TP*AP*TP*GP*AP*CP*CP*TP*GP*AP*AP*GP*TP*GP*AP*CP*CP*T)-3'F,M18synthetic construct
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, H, I
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
965
Query on 965

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Download CCD File 
B, I
[3-(3-{[2-chloro-3-(trifluoromethyl)benzyl](2,2-diphenylethyl)amino}propoxy)phenyl]acetic acid
C33 H31 Cl F3 N O3
NAXSRXHZFIBFMI-UHFFFAOYSA-N
 Ligand Interaction
9CR
Query on 9CR

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Download CCD File 
A, H
(9cis)-retinoic acid
C20 H28 O2
SHGAZHPCJJPHSC-ZVCIMWCZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.102 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.180 
  • Space Group: P 43
Unit Cell:
Length (Å)Angle (°)
a = 85.783α = 90.00
b = 85.783β = 90.00
c = 238.577γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
HKL-2000data collection
HKL-2000data reduction
PHASESphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-02-26
    Type: Initial release
  • Version 1.1: 2014-03-19
    Type: Database references
  • Version 1.2: 2016-11-09
    Type: Non-polymer description, Source and taxonomy