7AOS

crystal structure of the RARalpha/RXRalpha ligand binding domain heterodimer in complex with a fragment of SRC1 coactivator

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.211 

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Literature

Structural Insights into the Interaction of the Intrinsically Disordered Co-activator TIF2 with Retinoic Acid Receptor Heterodimer (RXR/RAR).

Senicourt, L., le Maire, A., Allemand, F., Carvalho, J.E., Guee, L., Germain, P., Schubert, M., Bernado, P., Bourguet, W., Sibille, N.

(2021) J Mol Biol 433: 166899-166899

  • DOI: 10.1016/j.jmb.2021.166899
  • Primary Citation of Related Structures:  
    7AOS, 7APO, 7BK4

  • PubMed Abstract: 

    • Retinoic acid receptors (RARs) and retinoid X receptors (RXRs) form heterodimers that activate target gene transcription by recruiting co-activator complexes in response to ligand binding. The nuclear receptor (NR) co-activator TIF2 mediates this recruitment by interacting with the ligand-binding domain (LBD) of NRs trough the nuclear receptor interaction domain (TIF2 NRID ) containing three highly conserved α-helical LxxLL motifs (NR-boxes) ...

    Retinoic acid receptors (RARs) and retinoid X receptors (RXRs) form heterodimers that activate target gene transcription by recruiting co-activator complexes in response to ligand binding. The nuclear receptor (NR) co-activator TIF2 mediates this recruitment by interacting with the ligand-binding domain (LBD) of NRs trough the nuclear receptor interaction domain (TIF2 NRID ) containing three highly conserved α-helical LxxLL motifs (NR-boxes). The precise binding mode of this domain to RXR/RAR is not clear due to the disordered nature of TIF2. Here we present the structural characterization of TIF2 NRID by integrating several experimental (NMR, SAXS, Far-UV CD, SEC-MALS) and computational data. Collectively, the data are in agreement with a largely disordered protein with partially structured regions, including the NR-boxes and their flanking regions, which are evolutionary conserved. NMR and X-ray crystallographic data on TIF2 NRID in complex with RXR/RAR reveal a multisite binding of the three NR-boxes as well as an active role of their flanking regions in the interaction.

    Organizational Affiliation: 

    Centre de Biochimie Structurale (CBS), CNRS, INSERM, Univ Montpellier, Montpellier, France. Electronic address: nathalie.sibille@cbs.cnrs.fr.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Retinoic acid receptor RXR-alphaA238Mus musculusMutation(s): 0 
Gene Names: Rxra, Nr2b1
UniProt
Find proteins for P28700 (Mus musculus)
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Go to UniProtKB:  P28700
Entity Groups  
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UniProt GroupP28700
Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Retinoic acid receptor alphaB266Homo sapiensMutation(s): 0 
Gene Names: RARA, NR1B1
UniProt & NIH Common Fund Data Resources
Find proteins for P10276 (Homo sapiens)
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Go to UniProtKB:  P10276
PHAROS:  P10276
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UniProt GroupP10276
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear receptor coactivator 1C, D27Homo sapiensMutation(s): 0 
Gene Names: NCOA1, BHLHE74, SRC1
EC: 2.3.1.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q15788 (Homo sapiens)
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Go to UniProtKB:  Q15788
PHAROS:  Q15788
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UniProt GroupQ15788
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LG2
Query on LG2
Download Ideal Coordinates CCD File 
E [auth A]6-[1-(3,5,5,8,8-PENTAMETHYL-5,6,7,8-TETRAHYDRONAPHTHALEN-2-YL)CYCLOPROPYL]PYRIDINE-3-CARBOXYLIC ACID
C24 H29 N O2
SLXTWXQUEZSSTJ-UHFFFAOYSA-N		 Ligand Interaction
EQN
Query on EQN
Download Ideal Coordinates CCD File 
G [auth B]4-{[(5,5,8,8-tetramethyl-5,6,7,8-tetrahydronaphthalen-2-yl)carbonyl]amino}benzoic acid
C22 H25 N O3
SZWKGOZKRMMLAJ-UHFFFAOYSA-N		 Ligand Interaction
GOL
Query on GOL
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F [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.211 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.283α = 90
b = 108.283β = 90
c = 99.786γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Brazilian National Council for Scientific and Technological Development (CNPq)Brazil--

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-04
    Type: Initial release