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- EMDB-55736: Focused refinement map on N-terminus of mouse TRPM3 alpha 2 in co... -

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Basic information

Entry
Database: EMDB / ID: EMD-55736
TitleFocused refinement map on N-terminus of mouse TRPM3 alpha 2 in complex with antagonist Ononetin
Map dataLocal refinement, filtered
Sample
  • Complex: Tetrameric assembly of mouse TRPM3 alpha 2 with inhibitor Ononetin
KeywordsCa2+ channel Ononetin-bound Closed conformation / MEMBRANE PROTEIN
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.84 Å
AuthorsShkumatov AV / Schenck S / Brunner JD
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2026
Title: Stereoselectivity and functional plasticity of a common ligand-binding pocket in TRPM3.
Authors: Bahar Bazeli / Alexander V Shkumatov / Stephan Schenck / Jean-Christophe Vanherck / Annelies Janssens / Stéphane A H Spieser / Damien Marchand / Robbe Roelens / Patrick Chaltin / Arnaud ...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 /
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.
History
DepositionNov 17, 2025-
Header (metadata) releaseFeb 11, 2026-
Map releaseFeb 11, 2026-
UpdateAug 26, 2026-
Current statusAug 26, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55736.png

Downloads & links

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Map

FileDownload / File: emd_55736.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocal refinement, filtered
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.69 Å/pix.
x 500 pix.
= 346.5 Å		0.69 Å/pix.
x 500 pix.
= 346.5 Å		0.69 Å/pix.
x 500 pix.
= 346.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.693 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0458
Minimum - Maximum-0.49347013 - 0.59260505
Average (Standard dev.)0.000029245546 (±0.0033306463)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 346.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half A

Fileemd_55736_half_map_1.map
Annotationhalf A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half B

Fileemd_55736_half_map_2.map
Annotationhalf B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Tetrameric assembly of mouse TRPM3 alpha 2 with inhibitor Ononetin

EntireName: Tetrameric assembly of mouse TRPM3 alpha 2 with inhibitor Ononetin
Components
  • Complex: Tetrameric assembly of mouse TRPM3 alpha 2 with inhibitor Ononetin

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Supramolecule #1: Tetrameric assembly of mouse TRPM3 alpha 2 with inhibitor Ononetin

SupramoleculeName: Tetrameric assembly of mouse TRPM3 alpha 2 with inhibitor Ononetin
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 161 KDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.3 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
10.0 mMC8H17N2NaO4SHepes
150.0 mMNaClSodium chloride
0.0063 %C56H92O25Glycodiosgenin
10.0 uMC15H14O4Ononetin

Details: 10 mM Hepes pH 7.5, 150 mM NaCl, 0.063% Glycodiosgenin, 10 uM Ononetin
GridModel: Quantifoil R2/1 / Material: GOLD / Mesh: 300 / Support film - Material: GRAPHENE / Support film - topology: CONTINUOUS
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 279.15 K / Instrument: LEICA EM GP / Details: GP2.

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 62.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.0 µm / Nominal defocus min: 0.7000000000000001 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8dds

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 192696
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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