9QJ9

Crystal Structure of the Human Retinoid X Receptor DNA-Binding Domain Bound to Trim16 IR1 Response Element

Summary for 9QJ9

• Entry DOI: 10.2210/pdb9qj9/pdb
• Descriptor: Retinoic acid receptor RXR-alpha, DNA (5'-D(P*GP*GP*GP*GP*TP*CP*AP*TP*GP*AP*CP*CP*CP*T)-3'), ZINC ION, ... (4 entities in total)
• Functional Keywords: dna complex, transcription
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 4
• Total formula weight: 30585.85

Authors

Rochel, N. (deposition date: 2025-03-18, release date: 2026-01-28)

Primary citation

Tambones, I.,Sagar, A.,Vankova, P.,Loginov, D.,Carivenc, C.,Rochel, N.,Bourguet, W.,Man, P.,Bernado, P.,le Maire, A.
New structural insights into the control of the retinoic acid receptors RAR/RXR by DNA, ligands, and transcriptional coregulators.
Nucleic Acids Res., 53:-, 2025

PubMed Abstract: Retinoic acid receptors (RARs) are ligand-dependent transcription factors essential for various biological processes, including embryogenesis, differentiation, and apoptosis. RARs function as heterodimers with retinoid X receptors (RXRs) and regulate gene expression via retinoic acid response elements (RAREs). Their transcriptional activity is modulated by coregulators, with corepressors maintaining repression in the absence of ligand and coactivators enabling transcription upon ligand binding. Structural studies reveal that DNA binding induces conformational changes affecting coregulator interactions. However, the precise structural organization of RAR/RXR-coregulator complexes and the allosteric influence of DNA on receptor function remain incompletely understood. Our study presents an integrative analysis of the RAR/RXR heterodimer bound to four distinct and relevant RAREs (DR0, DR1, DR5, and IR0) in complex with either a corepressor (NCoR) or a coactivator (TIF-2) nuclear receptor interaction domain. By combining small-angle X-ray scattering, hydrogen/deuterium exchange mass spectrometry, and molecular dynamics simulations, we revealed that the heterodimer adopts distinct conformations depending on the DNA sequence, influencing interdomain distances and receptor interactions. Additionally, we uncovered the dynamic interplay between ligand, DNA, and coregulator binding. This study provides new insights into the structural features of coregulator proteins and highlights the allosteric influence of RAREs on receptor function.

PubMed: 41036627
DOI: 10.1093/nar/gkaf967

Experimental method

X-RAY DIFFRACTION (3.5 Å)