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- EMDB-53174: Cryo-EM structure of mouse TRPM3 alpha 2 in APO state -

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Basic information

Entry
Database: EMDB / ID: EMD-53174
TitleCryo-EM structure of mouse TRPM3 alpha 2 in APO state
Map dataCryo-EM structure of mouse TRPM3 alpha 2 in APO state
Sample
  • Complex: Tetrameric assembly of mouse TRPM3 alpha 2
    • Protein or peptide: Transient receptor potential cation channel subfamily M member 3
  • Ligand: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
  • Ligand: CHOLESTEROL
KeywordsIon channel Ca2+ channel Ca2+ homeostasis / MEMBRANE PROTEIN
Function / homology
Function and homology information


zinc ion transmembrane transporter activity / zinc ion transmembrane transport / temperature-gated ion channel activity / sodium ion transport / monoatomic cation transport / phosphatidylinositol-4,5-bisphosphate binding / calcium ion transmembrane transport / calcium channel activity / G-protein beta/gamma-subunit complex binding / protein homotetramerization ...zinc ion transmembrane transporter activity / zinc ion transmembrane transport / temperature-gated ion channel activity / sodium ion transport / monoatomic cation transport / phosphatidylinositol-4,5-bisphosphate binding / calcium ion transmembrane transport / calcium channel activity / G-protein beta/gamma-subunit complex binding / protein homotetramerization / calmodulin binding / plasma membrane
Similarity search - Function
TRPM, tetramerisation domain / TRPM, tetramerisation domain superfamily / Tetramerisation domain of TRPM / : / TRPM, SLOG domain / : / SLOG in TRPM / TRPM2-like domain / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Transient receptor potential cation channel subfamily M member 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsShkumatov AV / Schenck S / Brunner JD
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of mouse TRPM3 alpha 2 in APO state
Authors: Shkumatov AV / Schenck S / Brunner JD
History
DepositionMar 16, 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_53174.png

Downloads & links

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Map

FileDownload / File: emd_53174.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of mouse TRPM3 alpha 2 in APO state
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.71 Å/pix.
x 500 pix.
= 355. Å		0.71 Å/pix.
x 500 pix.
= 355. Å		0.71 Å/pix.
x 500 pix.
= 355. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.71 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0411
Minimum - Maximum-0.096641235 - 0.22710973
Average (Standard dev.)0.00018912512 (±0.0074749175)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 355.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53174_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpened global map used for model building

Fileemd_53174_additional_1.map
AnnotationSharpened global map used for model building
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: DeepEMhancer map used for model building and refinement

Fileemd_53174_additional_2.map
AnnotationDeepEMhancer map used for model building and refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: halfA

Fileemd_53174_half_map_1.map
AnnotationhalfA
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: halfB

Fileemd_53174_half_map_2.map
AnnotationhalfB
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

EntireName: Tetrameric assembly of mouse TRPM3 alpha 2
Components
  • Complex: Tetrameric assembly of mouse TRPM3 alpha 2
    • Protein or peptide: Transient receptor potential cation channel subfamily M member 3
  • Ligand: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
  • Ligand: CHOLESTEROL

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Supramolecule #1: Tetrameric assembly of mouse TRPM3 alpha 2

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

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Macromolecule #1: Transient receptor potential cation channel subfamily M member 3

MacromoleculeName: Transient receptor potential cation channel subfamily M member 3
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse) / Strain: C57BL/6J
Molecular weightTheoretical: 136.145797 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: WIERAFYKRE CVHIIPSTKD PHRCCCGRLI GQHVGLTPSI SVLQNEKNES RLSRNDIQSE KWSISKHTQL SPTDAFGTIE FQGGGHSNK AMYVRVSFDT KPDLLLHLMT KEWQLELPKL LISVHGGLQN FELQPKLKQV FGKGLIKAAM TTGAWIFTGG V NTGVIRHV ...String:
WIERAFYKRE CVHIIPSTKD PHRCCCGRLI GQHVGLTPSI SVLQNEKNES RLSRNDIQSE KWSISKHTQL SPTDAFGTIE FQGGGHSNK AMYVRVSFDT KPDLLLHLMT KEWQLELPKL LISVHGGLQN FELQPKLKQV FGKGLIKAAM TTGAWIFTGG V NTGVIRHV GDALKDHASK SRGKICTIGI APWGIVENQE DLIGRDVVRP YQTMSNPMSK LTVLNSMHSH FILADNGTTG KY GAEVKLR RQLEKHISLQ KINTRIGQGV PVVALIVEGG PNVISIVLEY LRDTPPVPVV VCDGSGRASD ILAFGHKYSE EGG LINESL RDQLLVTIQK TFTYTRTQAQ HLFIILMECM KKKELITVFR MGSEGHQDID LAILTALLKG ANASAPDQLS LALA WNRVD IARSQIFIYG QQWPVGSLEQ AMLDALVLDR VDFVKLLIEN GVSMHRFLTI SRLEELYNTR HGPSNTLYHL VRDVK KGNL PPDYRISLID IGLVIEYLMG GAYRCNYTRK RFRTLYHNLF GPKRPKALKL LGMEDDIPLR RGRKTTKKRE EEVDID LDD PEINHFPFPF HELMVWAVLM KRQKMALFFW QHGEEAMAKA LVACKLCKAM AHEASENDMV DDISQELNHN SRDFGQL AV ELLDQSYKQD EQLAMKLLTY ELKNWSNATC LQLAVAAKHR DFIAHTCSQM LLTDMWMGRL RMRKNSGLKV ILGILLPP S ILSLEFKNKD DMPYMTQAQE IHLQEKEPEE PEKPTKEKDE EDMELTAMLG RSNGESSRKK DEEEVQSRHR LIPVGRKIY EFYNAPIVKF WFYTLAYIGY LMLFNYIVLV KMERWPSTQE WIVISYIFTL GIEKMREILM SEPGKLLQKV KVWLQEYWNV TDLIAILLF SVGMILRLQD QPFRSDGRVI YCVNIIYWYI RLLDIFGVNK YLGPYVMMIG KMMIDMMYFV IIMLVVLMSF G VARQAILF PNEEPSWKLA KNIFYMPYWM IYGEVFADQI DPPCGQNETR EDGKTIQLPP CKTGAWIVPA IMACYLLVAN IL LVNLLIA VFNNTFFEVK SISNQVWKFQ RYQLIMTFHE RPVLPPPLII FSHMTMIFQH VCCRWRKHES DQDERDYGLK LFI TDDELK KVHDFEEQCI EEYFREKDDR FNSSNDERIR VTSERVENMS MRLEEVNERE H

UniProtKB: Transient receptor potential cation channel subfamily M member 3

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Macromolecule #2: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE

MacromoleculeName: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / type: ligand / ID: 2 / Number of copies: 4 / Formula: 3PH
Molecular weightTheoretical: 704.998 Da
Chemical component information

ChemComp-3PH:
1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE

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Macromolecule #3: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 3 / Number of copies: 4 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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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

Concentration0.1 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
10.0 mMC8H17N2NaO4SHepes
150.0 mMNaClSodium chloride
0.0063 %C56H92O25Glycodiosgenin

Details: 10 mM Hepes pH 7.5, 150 mM NaCl, 0.063% Glycodiosgenin
GridModel: Quantifoil R2/1 / Material: GOLD / Mesh: 300 / Support film - Material: GRAPHENE / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 298.15 K / Instrument: GATAN CRYOPLUNGE 3

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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: 1.6 µm / Nominal defocus min: 0.7000000000000001 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 158322
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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