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

PDB DOI: 10.2210/pdb1XDK/pdb

Classification: HORMONE/GROWTH FACTOR RECEPTOR
Organism(s): Mus musculus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2004-09-07 Released: 2004-11-09
Deposition Author(s): 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.

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

Ligand Structure Quality Assessment

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

PubMed: 15528208 Search on PubMed
DOI: 10.1074/jbc.M409302200
Primary Citation of Related Structures:
1XDK

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 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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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Retinoic acid receptor RXR-alpha	A, E	238	Mus musculus	Mutation(s): 0 Gene Names: Rxra, Nr2b1
UniProt
Find proteins for P28700 (Mus musculus) Explore P28700 Go to UniProtKB: P28700
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P28700
Protein Feature View Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Retinoic acid receptor, beta	B, F	303	Mus musculus	Mutation(s): 0 Gene Names: Rarb, Nr1b2
UniProt
Find proteins for P22605 (Mus musculus) Explore P22605 Go to UniProtKB: P22605
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P22605
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Thyroid Receptor Associated Protein 220	C, D, G, H	14	N/A	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q925J9 (Mus musculus) Explore Q925J9 Go to UniProtKB: Q925J9
IMPC: MGI:1100846
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q925J9
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
9CR Query on 9CR Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth B] SDF format, chain L [auth F] SDF format, chain K [auth E] MOL2 format, chain I [auth A] MOL2 format, chain J [auth B] MOL2 format, chain L [auth F] MOL2 format, chain K [auth E]	I [auth A], J [auth B], K [auth E], L [auth F]	(9cis)-retinoic acid C₂₀ H₂₈ O₂ SHGAZHPCJJPHSC-ZVCIMWCZSA-N		Ligand Interaction

Binding Affinity Annotations
ID	Source	Binding Affinity
9CR	BindingDB: 1XDK	Ki: min: 0.5, max: 583 (nM) from 16 assay(s)
		Kd: min: 0.2, max: 1810 (nM) from 29 assay(s)
		IC50: min: 4, max: 82 (nM) from 8 assay(s)
		EC50: min: 1.5, max: 316 (nM) from 34 assay(s)