1XDK

Crystal Structure of the RARbeta/RXRalpha Ligand Binding Domain Heterodimer in Complex with 9-cis Retinoic Acid and a Fragment of the TRAP220 Coactivator

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.253 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history. 


Literature

CHARACTERIZATION OF THE INTERACTION BETWEEN RAR/RXR HETERODIMERS AND TRANSCRIPTIONAL COACTIVATORS THROUGH STRUCTURAL AND FLUORESCENCE ANISOTROPY STUDIES

Pogenberg, V., Guichou, J.F., Vivat-Hannah, V., Kammerer, S., Perez, E., Germain, P., De Lera, A.R., Gronemeyer, H., Royer, C.A., Bourguet, W.

(2005) J Biol Chem 280: 1625-1633

  • DOI: 10.1074/jbc.M409302200
  • Structures With Same Primary Citation

  • PubMed Abstract: 

    • Retinoid receptors (RARs and RXRs) are ligand-activated transcription factors that regulate the transcription of target genes by recruiting coregulator complexes at cognate promoters. To understand the effects of heterodimerization and ligand binding ...

    Retinoid receptors (RARs and RXRs) are ligand-activated transcription factors that regulate the transcription of target genes by recruiting coregulator complexes at cognate promoters. To understand the effects of heterodimerization and ligand binding on coactivator recruitment, we solved the crystal structure of the complex between the RARbeta/RXRalpha ligand-binding domain heterodimer, its 9-cis retinoic acid ligand, and an LXXLL-containing peptide (termed NR box 2) derived from the nuclear receptor interaction domain (NID) of the TRAP220 coactivator. In parallel, we measured the binding affinities of the isolated NR box 2 peptide or the full-length NID of the coactivator SRC-1 for retinoid receptors in the presence of various types of ligands. Our correlative analysis of three-dimensional structures and fluorescence data reveals that heterodimerization does not significantly alter the structure of individual subunits or their intrinsic capacity to interact with NR box 2. Similarly, we show that the ability of a protomer to recruit NR box 2 does not vary as a function of the ligand binding status of the partner receptor. In contrast, the strength of the overall association between the heterodimer and the full-length SRC-1 NID is dictated by the combinatorial action of RAR and RXR ligands, the simultaneous presence of the two receptor agonists being required for highest binding affinity. We identified an LXXLL peptide-driven mechanism by which the concerted reorientation of three phenylalanine side chains generates an "aromatic clamp" that locks the RXR activation helix H12 in the transcriptionally active conformation. Finally, we show how variations of helix H11-ligand interactions can alter the communication pathway linking helices H11, H12, and the connecting loop L11-12 to the coactivator-binding site. Together, our results reveal molecular and structural features that impact on the ligand-dependent interaction of the RAR/RXR heterodimer with nuclear receptor coactivators.

    Organizational Affiliation: 

    Centre de Biochimie Structurale, CNRS U5048-INSERM U554-UM1, Faculté de Pharmacie, 15 avenue Charles Flahault, 34093 Montpellier, France.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Retinoic acid receptor RXR-alphaA, E238Mus musculusMutation(s): 0 
Gene Names: Rxra, Nr2b1
Find proteins for P28700 (Mus musculus)
Explore P28700 
Go to UniProtKB:  P28700
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Retinoic acid receptor, betaB, F303Mus musculusMutation(s): 0 
Gene Names: Rarb, Nr1b2
Find proteins for P22605 (Mus musculus)
Explore P22605 
Go to UniProtKB:  P22605
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Thyroid Receptor Associated Protein 220C, D, G, H14N/AMutation(s): 0 
Find proteins for Q925J9 (Mus musculus)
Explore Q925J9 
Go to UniProtKB:  Q925J9
NIH Common Fund Data Resources
IMPC  MGI:1100846
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9CR
Query on 9CR
Download CCD File 
A, B, E, F
(9cis)-retinoic acid
C20 H28 O2
SHGAZHPCJJPHSC-ZVCIMWCZSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
9CRKi:  0.5   nM  BindingDB
9CRIC50:  12   nM  BindingDB
9CRKd:  4   nM  BindingDB
9CREC50:  4.5   nM  BindingDB
9CRIC50:  31   nM  BindingDB
9CRKd:  30   nM  BindingDB
9CREC50:  10   nM  BindingDB
9CRKi:  3.799999952316284   nM  BindingDB
9CREC50:  29   nM  BindingDB
9CRKd:  7   nM  BindingDB
9CREC50:  13   nM  BindingDB
9CRKd:  16   nM  BindingDB
9CRKi:  8   nM  BindingDB
9CRKd:  15   nM  BindingDB
9CRKd:  14   nM  BindingDB
9CRKd:  7   nM  BindingDB
9CRKd:  240   nM  BindingDB
9CRKi:  12   nM  BindingDB
9CREC50:  2.5999999046325684   nM  BindingDB
9CRKi:  0.699999988079071   nM  BindingDB
9CREC50:  304   nM  BindingDB
9CREC50:  200   nM  BindingDB
9CRIC50:  7   nM  BindingDB
9CRKd:  12   nM  BindingDB
9CRKd:  11   nM  BindingDB
9CRKd:  1.5   nM  BindingDB
9CREC50:  100   nM  BindingDB
9CREC50:  140   nM  BindingDB
9CRKd:  7   nM  BindingDB
9CREC50:  52   nM  BindingDB
9CREC50:  128   nM  BindingDB
9CREC50:  200   nM  BindingDB
9CRKd:  11   nM  BindingDB
9CREC50:  50   nM  BindingDB
9CREC50:  219   nM  BindingDB
9CREC50:  220   nM  BindingDB
9CREC50:  120   nM  BindingDB
9CREC50:  191   nM  BindingDB
9CRIC50:  4   nM  BindingDB
9CREC50:  110   nM  BindingDB
9CREC50:  124   nM  BindingDB
9CRKd:  3   nM  BindingDB
9CREC50:  22   nM  BindingDB
9CRKi:  8.399999618530273   nM  BindingDB
9CREC50:  195   nM  BindingDB
9CRKi:  27   nM  BindingDB
9CRKd:  1810   nM  BindingDB
9CREC50:  102   nM  BindingDB
9CREC50:  250   nM  BindingDB
9CREC50:  29   nM  BindingDB
9CRKd:  15   nM  BindingDB
9CRKd:  1560   nM  BindingDB
9CRKd:  32   nM  BindingDB
9CREC50:  1.5   nM  BindingDB
9CRKi:  14   nM  BindingDB
9CRKd:  35   nM  BindingDB
9CRKi:  7.400000095367432   nM  BindingDB
9CRKd:  9   nM  BindingDB
9CRKd:  97   nM  BindingDB
9CRKd:  100   nM  BindingDB
9CREC50:  316   nM  BindingDB
9CRKd:  8   nM  BindingDB
9CRKi:  22   nM  BindingDB
9CRKi:  11   nM  BindingDB
9CRKd:  14   nM  BindingDB
9CRKd:  13   nM  BindingDB
9CREC50:  4.300000190734863   nM  BindingDB
9CREC50:  3.299999952316284   nM  BindingDB
9CRIC50:  7   nM  BindingDB
9CREC50:  45   nM  BindingDB
9CREC50:  21   nM  BindingDB
9CRKi:  11   nM  BindingDB
9CRKd:  0.20000000298023224   nM  BindingDB
9CRKi:  13   nM  BindingDB
9CREC50:  23   nM  BindingDB
9CRKi:  9   nM  BindingDB
9CREC50:  6   nM  BindingDB
9CRIC50:  32   nM  BindingDB
9CRIC50:  82   nM  BindingDB
9CREC50:  3   nM  BindingDB
9CRIC50:  29   nM  BindingDB
9CRKd:  90   nM  BindingDB
9CRKd:  93   nM  BindingDB
9CRKd:  50   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.253 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.7α = 90
b = 115.7β = 90
c = 247.2γ = 120
Software Package:
Software NamePurpose
MAR345data collection
SCALAdata scaling
MOLREPphasing
CNSrefinement
MOSFLMdata reduction
CCP4data scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-11-09
    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: 2016-11-16
    Changes: Non-polymer description
  • Version 1.4: 2017-10-11
    Changes: Refinement description