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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: To Be Published
Title: Focused refinement map on N-terminus of mouse TRPM3 alpha 2 in complex with antagonist Ononetin
Authors: Shkumatov AV / Schenck S / Brunner JD
History
DepositionNov 17, 2025-
Header (metadata) releaseFeb 11, 2026-
Map releaseFeb 11, 2026-
UpdateFeb 11, 2026-
Current statusFeb 11, 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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