1XIU: Crystal Structure Of The Agonist-bound Ligand-binding Domain Of Biomphalaria Glabrata Rxr

Nuclear receptors form an important class of transcription regulators in metazoans. To learn more about the evolution of these proteins, we have initiated structural studies on nuclear receptor ligand-binding domains from various animals. Here we present the crystal structure of the ligand-binding domain (LBD) of the retinoid X receptor (RXR) from the mollusc Biomphalaria glabrata. The structure reveals a novel tetrameric association in which each monomer is complexed to the human RXR ligand 9-cis retinoic acid and to a human co-activator-derived peptide. The ligand and the co-activator peptide are bound in essentially the same manner as observed in previously reported human RXR LBD structures, suggesting that the mechanisms of RXR-mediated transcription regulation are very similar in mollusc and human. The structure shows further that binding of ligand and co-activator peptide does not necessarily lead to the typical holo-conformation in which helix 12 (H12) folds back and packs against the LBD. Within a canonical dimer, only one monomer is in this closed agonist conformation. The other monomer is in an open conformation with H12 protruding from the LBD core, occupying the H12 interaction groove of another open monomer in an adjacent dimer in a domain swapping fashion, thus resulting in a tetrameric association. Additional tetramer interfaces are formed between H11 of the closed LBD and H6 of the open LBD. This novel holo-tetramer configuration may have a biological role in activating genes whose promoters are poorly recognised by dimers but much more efficiently by the corresponding tetramers.
PDB ID: 1XIUDownload
MMDB ID: 35043
PDB Deposition Date: 2004/9/22
Updated in MMDB: 2016/11
Experimental Method:
x-ray diffraction
Resolution: 2.5  Å
Source Organism:
Biomphalaria glabrata
Similar Structures:
Biological Unit for 1XIU: octameric; determined by author
Molecular Components in 1XIU
Label Count Molecule
Proteins (8 molecules)
Rxr-like Protein
Molecule annotation
Nuclear Receptor Coactivator 1(Gene symbol: NCOA1)
Molecule annotation
Chemicals (4 molecules)
* Click molecule labels to explore molecular sequence information.

Citing MMDB