6SSQ

Crystal structure of RARbeta LBD in complex with LG 100754


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.162 

wwPDB Validation 3D Report Full Report



Literature

Regulation of RXR-RAR Heterodimers by RXR- and RAR-Specific Ligands and Their Combinations.

le Maire, A.Teyssier, C.Balaguer, P.Bourguet, W.Germain, P.

(2019) Cells 8

  • DOI: 10.3390/cells8111392
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The three subtypes (α, β, and γ) of the retinoic acid receptor (RAR) are ligand-dependent transcription factors that mediate retinoic acid signaling by forming heterodimers with the retinoid X receptor (RXR). Heterodimers are functional units that bi ...

    The three subtypes (α, β, and γ) of the retinoic acid receptor (RAR) are ligand-dependent transcription factors that mediate retinoic acid signaling by forming heterodimers with the retinoid X receptor (RXR). Heterodimers are functional units that bind ligands (retinoids), transcriptional co-regulators and DNA, to regulate gene networks controlling cell growth, differentiation, and death. Using biochemical, crystallographic, and cellular approaches, we have set out to explore the spectrum of possibilities to regulate RXR-RAR heterodimer-dependent transcription through various pharmacological classes of RAR- and RXR- specific ligands, alone or in combination. We reveal the molecular details by which these compounds direct specificity and functionality of RXR-RAR heterodimers. Among these ligands, we have reevaluated and improved the molecular and structural definition of compounds CD2665, Ro41-5253, LE135, or LG100754, highlighting novel functional features of these molecules. Our analysis reveals a model of RXR-RAR heterodimer action in which each subunit retains its intrinsic properties in terms of ligand and co-regulator binding. However, their interplay upon the combined action of RAR- and RXR-ligands allows for the fine tuning of heterodimer activity. It also stresses the importance of accurate ligand characterization to use synthetic selective retinoids appropriately and avoid data misinterpretations.


    Organizational Affiliation

    Centre de Biochimie Structurale (CBS), CNRS, INSERM, University of Montpellier, 34090 Montpellier, France.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Retinoic acid receptor beta
A, B
267Homo sapiensMutation(s): 0 
Gene Names: RARBHAPNR1B2
Find proteins for P10826 (Homo sapiens)
Go to UniProtKB:  P10826
NIH Common Fund Data Resources
PHAROS  P10826
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nuclear receptor coactivator 1
F, G
13Homo sapiensMutation(s): 0 
Gene Names: NCOA1BHLHE74SRC1
EC: 2.3.1.48
Find proteins for Q15788 (Homo sapiens)
Go to UniProtKB:  Q15788
NIH Common Fund Data Resources
PHAROS  Q15788
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
754
Query on 754

Download CCD File 
A, B
(2E,4E,6Z)-3-methyl-7-(5,5,8,8-tetramethyl-3-propoxy-5,6,7,8-tetrahydronaphthalen-2-yl)octa-2,4,6-trienoic acid
C26 H36 O3
HNODNXQAYXJFMQ-LQUSFLDPSA-N
 Ligand Interaction
FLC
Query on FLC

Download CCD File 
A
CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
754Ki:  6094   nM  BindingDB
754Ki:  1791   nM  BindingDB
754EC50:  10   nM  BindingDB
754Ki:  2587   nM  BindingDB
754EC50:  192   nM  BindingDB
754EC50:  4   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.162 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.209α = 90
b = 85.296β = 90
c = 109.29γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-11-20
    Type: Initial release