1XLS

Crystal structure of the mouse CAR/RXR LBD heterodimer bound to TCPOBOP and 9cRA and a TIF2 peptide containg the third LXXLL motifs


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.96 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.255 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

The nuclear xenobiotic receptor CAR: structural determinants of constitutive activation and heterodimerization.

Suino, K.Peng, L.Reynolds, R.Li, Y.Cha, J.Y.Repa, J.J.Kliewer, S.A.Xu, H.E.

(2004) Mol Cell 16: 893-905

  • DOI: 10.1016/j.molcel.2004.11.036
  • Primary Citation of Related Structures:  
    1XLS

  • PubMed Abstract: 
  • Constitutive androstane receptor (CAR) induces xenobiotic, bilirubin, and thyroid hormone metabolism as a heterodimer with the retinoid X receptor (RXR). Unlike ligand-dependent nuclear receptors, CAR is constitutively active. Here, we report the het ...

    Constitutive androstane receptor (CAR) induces xenobiotic, bilirubin, and thyroid hormone metabolism as a heterodimer with the retinoid X receptor (RXR). Unlike ligand-dependent nuclear receptors, CAR is constitutively active. Here, we report the heterodimeric structure of the CAR and RXR ligand binding domains (LBDs), which reveals an unusually large dimerization interface and a small CAR ligand binding pocket. Constitutive CAR activity appears to be mediated by the compact nature of the CAR LBD that displays several unique features including a shortened AF2 helix and helix H10, which are linked by a two-turn helix that normally adopts an extended loop in other receptors, and an extended helix H2 that stabilizes the canonical LBD fold by packing tightly against helix H3. These structural observations provide a molecular framework for understanding the atypical transcriptional activation properties of CAR.


    Organizational Affiliation

    Laboratory of Structural Sciences, Van Andel Research Institute, 333 Bostwick Avenue, Grand Rapids, MI 49503, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Retinoic acid receptor RXR-alphaABCD232Homo sapiensMutation(s): 0 
Gene Names: humanRXRANR2B1
Find proteins for P19793 (Homo sapiens)
Explore P19793 
Go to UniProtKB:  P19793
NIH Common Fund Data Resources
PHAROS  P19793
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Orphan nuclear receptor NR1I3EFGH242Mus musculusMutation(s): 0 
Gene Names: mouseNr1i3Car
Find proteins for O35627 (Mus musculus)
Explore O35627 
Go to UniProtKB:  O35627
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear receptor coactivator 2IJKLMNOP18Rattus norvegicusMutation(s): 0 
Gene Names: Ncoa2Tif2
Find proteins for Q9WUI9 (Rattus norvegicus)
Explore Q9WUI9 
Go to UniProtKB:  Q9WUI9
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TCD
Query on TCD

Download CCD File 
E, F, G, H
3,5-DICHLORO-2-{4-[(3,5-DICHLOROPYRIDIN-2-YL)OXY]PHENOXY}PYRIDINE
C16 H8 Cl4 N2 O2
BAFKRPOFIYPKBQ-UHFFFAOYSA-N
 Ligand Interaction
9CR
Query on 9CR

Download CCD File 
A, B, C, D
(9cis)-retinoic acid
C20 H28 O2
SHGAZHPCJJPHSC-ZVCIMWCZSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
9CRKd:  15   nM  BindingDB
9CRKd:  14   nM  BindingDB
9CREC50:  6   nM  BindingDB
9CREC50:  120   nM  BindingDB
9CRKd:  16   nM  BindingDB
9CRKd:  11   nM  BindingDB
9CREC50:  200   nM  BindingDB
9CRKd:  12   nM  BindingDB
9CRKd:  30   nM  BindingDB
9CRIC50:  82   nM  BindingDB
9CRKd:  35   nM  BindingDB
9CREC50:  4.5   nM  BindingDB
9CRKd:  14   nM  BindingDB
9CRKi:  7.400000095367432   nM  BindingDB
9CRKd:  13   nM  BindingDB
9CRKi:  8   nM  BindingDB
9CREC50:  4.300000190734863   nM  BindingDB
9CREC50:  13   nM  BindingDB
9CRKd:  32   nM  BindingDB
9CREC50:  10   nM  BindingDB
9CRKi:  9   nM  BindingDB
9CRKd:  50   nM  BindingDB
9CRKi:  14   nM  BindingDB
9CRKi:  3.799999952316284   nM  BindingDB
9CREC50:  100   nM  BindingDB
9CRIC50:  29   nM  BindingDB
9CRIC50:  32   nM  BindingDB
9CRKi:  11   nM  BindingDB
9CRIC50:  12   nM  BindingDB
9CRKd:  1.5   nM  BindingDB
9CREC50:  29   nM  BindingDB
9CRKi:  13   nM  BindingDB
9CRKi:  27   nM  BindingDB
9CRKi:  12   nM  BindingDB
9CREC50:  2.5999999046325684   nM  BindingDB
9CRKd:  240   nM  BindingDB
9CRKi:  8.399999618530273   nM  BindingDB
9CREC50:  128   nM  BindingDB
9CREC50:  1.5   nM  BindingDB
9CRKd:  8   nM  BindingDB
9CREC50:  316   nM  BindingDB
9CRKd:  9   nM  BindingDB
9CREC50:  140   nM  BindingDB
9CRKd:  1810   nM  BindingDB
9CREC50:  250   nM  BindingDB
9CRKd:  1560   nM  BindingDB
9CREC50:  124   nM  BindingDB
9CREC50:  195   nM  BindingDB
9CRIC50:  4   nM  BindingDB
9CREC50:  110   nM  BindingDB
9CREC50:  120   nM  BindingDB
9CREC50:  200   nM  BindingDB
9CRKd:  3   nM  BindingDB
9CRKd:  4   nM  BindingDB
9CREC50:  219   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.96 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.255 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.271α = 79.02
b = 88.381β = 85.81
c = 105.494γ = 67.22
Software Package:
Software NamePurpose
CNSrefinement
MAR345data collection
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-12-28
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2016-11-09
    Changes: Non-polymer description, Source and taxonomy
  • Version 1.4: 2017-10-11
    Changes: Refinement description