7W2D

The closed conformation of the sigma-1 receptor from Xenopus laevis complexed with S1RA

Summary for 7W2D

• Entry DOI: 10.2210/pdb7w2d/pdb
• Descriptor: Sigma non-opioid intracellular receptor 1, GOLD ION, 4-[2-(5-methyl-1-naphthalen-2-yl-pyrazol-3-yl)oxyethyl]morpholine (3 entities in total)
• Functional Keywords: sigma receptor, membrane receptor, s1r, ligand entry, membrane protein
• Biological source: Xenopus laevis (African clawed frog)
• Total number of polymer chains: 12
• Total formula weight: 310236.38

Authors

Meng, F.,Sun, Z.,Zhou, X. (deposition date: 2021-11-23, release date: 2022-03-16, Last modification date: 2023-11-29)

Primary citation

Meng, F.,Xiao, Y.,Ji, Y.,Sun, Z.,Zhou, X.
An open-like conformation of the sigma-1 receptor reveals its ligand entry pathway.
Nat Commun, 13:1267-1267, 2022

PubMed Abstract: The sigma-1 receptor (σR) is a non-opioid transmembrane receptor which has been implicated in many diseases, including neurodegenerative disorders and cancer. After more than forty years of research, substantial progress has been made in understanding this unique receptor, yet the molecular mechanism of its ligand entry pathway remains uncertain. Published structures of human σR reveal its homotrimeric organization of a cupin-fold β-barrel body that contains the ligand binding site, a carboxy-terminal V-shaped two-helix bundle, and a single amino-terminal transmembrane helix, while simulation studies have suggested a ligand entry pathway that is generated by conformational rearrangements of the cupin-fold domain. Here, we present multiple crystal structures, including an open-like conformation, of σR from Xenopus laevis. Together with functional binding analysis our data suggest that access to the σR ligand binding site is likely achieved by protein conformational changes that involve the carboxy-terminal two-helix bundle, rather than structural changes in the cupin-fold domain.

PubMed: 35273182
DOI: 10.1038/s41467-022-28946-w

Experimental method

X-RAY DIFFRACTION (3.471 Å)