1BY4

STRUCTURE AND MECHANISM OF THE HOMODIMERIC ASSEMBLY OF THE RXR ON DNA

Summary for 1BY4

• Entry DOI: 10.2210/pdb1by4/pdb
• Descriptor: DNA (5'-D(*C*TP*AP*GP*GP*TP*CP*AP*AP*AP*GP*GP*TP*CP*AP*G)-3'), DNA (5'-D(*CP*TP*GP*AP*CP*CP*TP*TP*TP*GP*AP*CP*CP*TP*A)-3'), PROTEIN (RETINOIC ACID RECEPTOR RXR-ALPHA), ... (5 entities in total)
• Functional Keywords: rxr, nuclear receptor, hormone response element, protein-dna interations, gene regulation-dna complex, gene regulation/dna
• Biological source: Homo sapiens (human)
• Cellular location: Nucleus: P19793
• Total number of polymer chains: 8
• Total formula weight: 58062.46

Authors

Zhao, Q.,Chasse, S.A.,Devarakonda, S.,Sierk, M.L.,Ahvazi, B.,Sigler, P.B.,Rastinejad, F. (deposition date: 1998-10-22, release date: 2000-01-12, Last modification date: 2023-08-09)

Primary citation

Zhao, Q.,Chasse, S.A.,Devarakonda, S.,Sierk, M.L.,Ahvazi, B.,Rastinejad, F.
Structural basis of RXR-DNA interactions.
J.Mol.Biol., 296:509-520, 2000

PubMed Abstract: The 9-cis retinoic acid receptor, RXR, binds DNA effectively as a homodimer or as a heterodimer with other nuclear receptors. The DNA-binding sites for these RXR complexes are direct repeats of a consensus sequence separated by one to five base-pairs of intervening space. Here, we report the 2.1 A crystal structure of the RXR-DNA-binding domain as a homodimer in complex with its idealized direct repeat DNA target. The structure shows how a gene-regulatory site can induce conformational changes in a transcription factor that promote homo-cooperative assembly. Specifically, an alpha-helix in the T-box is disrupted to allow efficient DNA-binding and subunit dimerization. RXR displays a relaxed mode of sequence recognition, interacting with only three base-pairs in each hexameric half-site. The structure illustrates how site selection is achieved in this large eukaryotic transcription factor family through discrete protein-protein interactions and the use of tandem DNA binding sites with characteristic spacings.

PubMed: 10669605
DOI: 10.1006/jmbi.1999.3457

Experimental method

X-RAY DIFFRACTION (2.1 Å)