Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
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Journal
IF	>30 >20 >10 >5 all

Title	Stereoselectivity and functional plasticity of a common ligand-binding pocket in TRPM3.
Journal, issue, pages	Nat Commun, Vol. 17, Issue 1, Year 2026
Publish date	Apr 1, 2026
Authors	Bahar Bazeli / Alexander V Shkumatov / Stephan Schenck / Jean-Christophe Vanherck / Annelies Janssens / Stéphane A H Spieser / Damien Marchand / Robbe Roelens / Patrick Chaltin / Arnaud Marchand / Joris Vriens / Thomas Voets / Janine D Brunner /
PubMed Abstract	The transient receptor potential melastatin 3 (TRPM3) channel is a key mediator of peripheral pain signaling, and pathogenic mutations in TRPM3 are linked to neurodevelopmental delay and epilepsy. ...The transient receptor potential melastatin 3 (TRPM3) channel is a key mediator of peripheral pain signaling, and pathogenic mutations in TRPM3 are linked to neurodevelopmental delay and epilepsy. Despite the therapeutic promise of TRPM3 modulators, the molecular mechanisms by which ligands modulate channel gating remain poorly understood. Here, we combine cryo-electron microscopy (cryo-EM) with functional analyses to characterize a promiscuous ligand-binding pocket formed by transmembrane helices S1-S4. This pocket accommodates several chemically diverse plant-derived and synthetic agonists and antagonists. We show stereoselectivity of TRPM3 for the (R)-enantiomer of the flavonoid antagonist isosakuranetin and the (R)-enantiomer of the synthetic agonist CIM0216. Mutations within this pocket-including variants identified in patients -alter ligand affinity and, in some cases, invert the functional outcome of ligand binding. These findings reveal the stereoselectivity and functional plasticity of the TRPM3 ligand-binding pocket, highlighting how subtle changes in the molecular interactions can produce divergent effects on channel gating, with important ramifications for TRPM3-targeted drug development and therapy.
External links	Nat Commun / PubMed:41922314 / PubMed Central
Methods	EM (single particle)
Resolution	2.35 - 3.28 Å
Structure data	53173 9qhm EMDB-53173, PDB-9qhm: Cryo-EM structure of mouse TRPM3 alpha 2 in complex with antagonist Ononetin Method: EM (single particle) / Resolution: 2.61 Å 53174 9qhn EMDB-53174, PDB-9qhn: Cryo-EM structure of mouse TRPM3 alpha 2 in APO state Method: EM (single particle) / Resolution: 3.2 Å 53175 9qho EMDB-53175, PDB-9qho: Cryo-EM structure of mouse TRPM3 alpha 2 in complex with antagonist Primidone Method: EM (single particle) / Resolution: 3.28 Å 53176 9qhp EMDB-53176, PDB-9qhp: Cryo-EM structure of mouse TRPM3 alpha 2 in complex with antagonist Isosakuranetin Method: EM (single particle) / Resolution: 2.35 Å 53177 9qhq EMDB-53177, PDB-9qhq: Cryo-EM structure of mouse TRPM3 alpha 2 in with agonists CIM-0216 and Pregnenolone sulfate (PregS) Method: EM (single particle) / Resolution: 3.07 Å EMDB-55736: Focused refinement map on N-terminus of mouse TRPM3 alpha 2 in complex with antagonist Ononetin Method: EM (single particle) / Resolution: 2.84 Å 55737 9t9u EMDB-55737, PDB-9t9u: Cryo-EM composite structure of mouse TRPM3 alpha 2 in complex with antagonist Ononetin Method: EM (single particle) / Resolution: 2.61 Å
Chemicals	PDB-1d6m: CRYSTAL STRUCTURE OF E. COLI DNA TOPOISOMERASE III ChemComp-3PH: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE ChemComp-YUV: (25R)-14beta,17beta-spirost-5-en-3beta-ol ChemComp-CLR: CHOLESTEROL ChemComp-9Z9: (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en / detergentYM PDB-1aia: STRUCTURAL BASIS FOR THE CATALYTIC ACTIVITY OF ASPARTATE AMINOTRANSFERASE K258H LACKING THE PYRIDOXAL-5'-PHOSPHATE BINDING LYSINE RESIDUE ChemComp-PX8: 1,2-DISTEAROYL-SN-GLYCERO-3-PHOSPHATE PDB-1jbk: Crystal Structure of the First Nucelotide Binding Domain of ClpB PDB-1i8p: STRUCTURE DETERMINATION OF THE FERROCYTOCHROME C2 FROM RHODOPSEUDOMONAS PALUSTRIS ChemComp-A8W: Pregnenolone sulfate / antidepressantYM
Source	mus musculus (house mouse)
Keywords	MEMBRANE PROTEIN / Ca2+ channel Ononetin-bound Closed conformation / Ion channel Ca2+ channel Ca2+ homeostasis / Ca2+ channel Primidone-bound Closed conformation / Ca2+ channel / Isosakuranetin-bound Closed conformation / Ca2+ channel CIM-0216-bound Pregnenolone sulfate-bound