4NQA

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.186 

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
  • Primary Citation of Related Structures:  
    4NQA

  • 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. [3] Department of Biosciences, Karolinska Institutet, Novum, Huddinge, Sweden.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Retinoic acid receptor RXR-alphaAH365Homo sapiensMutation(s): 0 
Gene Names: RXRANR2B1
Find proteins for P19793 (Homo sapiens)
Explore P19793 
Go to UniProtKB:  P19793
NIH Common Fund Data Resources
PHAROS  P19793
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Liver X nuclear receptor betaBI391Homo sapiensMutation(s): 0 
Gene Names: NR1H2hCG_22944LXRBNERUNR
Find proteins for P55055 (Homo sapiens)
Explore P55055 
Go to UniProtKB:  P55055
NIH Common Fund Data Resources
PHAROS  P55055
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear receptor coactivator 2CDJK13Homo sapiensMutation(s): 0 
Gene Names: NCOA2BHLHE75TIF2SRC2
Find proteins for Q15596 (Homo sapiens)
Explore Q15596 
Go to UniProtKB:  Q15596
NIH Common Fund Data Resources
PHAROS  Q15596
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 4
    MoleculeChainsLengthOrganismImage
    5'-D(*TP*AP*AP*GP*GP*TP*CP*AP*CP*TP*TP*CP*AP*GP*GP*TP*CP*A)-3'E, L18synthetic construct
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 5
      MoleculeChainsLengthOrganismImage
      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
      965
      Query on 965

      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

      Download CCD File 
      A, H
      (9cis)-retinoic acid
      C20 H28 O2
      SHGAZHPCJJPHSC-ZVCIMWCZSA-N
       Ligand Interaction
      ZN
      Query on ZN

      Download CCD File 
      A, B, H, I
      ZINC ION
      Zn
      PTFCDOFLOPIGGS-UHFFFAOYSA-N
       Ligand Interaction
      External Ligand Annotations 
      IDBinding Affinity (Sequence Identity %)
      9CRKd:  32   nM  BindingDB
      9CRKd:  1.5   nM  BindingDB
      9CRKd:  240   nM  BindingDB
      9CREC50:  110   nM  BindingDB
      9CREC50:  1730   nM  BindingDB
      9CREC50:  120   nM  BindingDB
      9CREC50:  6   nM  BindingDB
      9CREC50:  100   nM  BindingDB
      9CRIC50:  29   nM  BindingDB
      9CRKd:  3   nM  BindingDB
      9CRKd:  50   nM  BindingDB
      9CREC50:  120   nM  BindingDB
      9CRIC50:  32   nM  BindingDB
      9CREC50:  195   nM  BindingDB
      9CRIC50:  82   nM  BindingDB
      9CREC50:  13   nM  BindingDB
      9CRKd:  1560   nM  BindingDB
      9CRKi:  8.399999618530273   nM  BindingDB
      9CREC50:  10   nM  BindingDB
      9CRKi:  8   nM  BindingDB
      9CREC50:  1.5   nM  BindingDB
      9CRKd:  13   nM  BindingDB
      9CRKd:  14   nM  BindingDB
      9CRKd:  1810   nM  BindingDB
      9CREC50:  250   nM  BindingDB
      9CRKi:  12   nM  BindingDB
      9CRKd:  8   nM  BindingDB
      9CREC50:  200   nM  BindingDB
      9CREC50:  316   nM  BindingDB
      9CRKd:  9   nM  BindingDB
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 3.10 Å
      • R-Value Free: 0.218 
      • R-Value Work: 0.180 
      • R-Value Observed: 0.186 
      • Space Group: P 43
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 85.783α = 90
      b = 85.783β = 90
      c = 238.577γ = 90
      Software Package:
      Software NamePurpose
      HKL-2000data collection
      PHASESphasing
      PHENIXrefinement
      HKL-2000data reduction
      HKL-2000data scaling

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History 

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