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- EMDB-53175: Cryo-EM structure of mouse TRPM3 alpha 2 in complex with antagoni... -

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Basic information

Entry
Database: EMDB / ID: EMD-53175
TitleCryo-EM structure of mouse TRPM3 alpha 2 in complex with antagonist Primidone
Map dataCryo-EM structure of mouse TRPM3 alpha 2 in complex with antagonist Primidone
Sample
  • Complex: Tetrameric assembly of mouse TRPM3 alpha 2 in complex with antagonist Primidone
    • Protein or peptide: MKIAA1616 protein
  • Ligand: (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en
  • Ligand: primidone
  • Ligand: 1,2-DISTEAROYL-SN-GLYCERO-3-PHOSPHATE
KeywordsCa2+ channel Primidone-bound Closed conformation / MEMBRANE PROTEIN
Function / homology
Function and homology information


protein tetramerization / calcium channel activity / 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: 3.28 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 complex with antagonist Primidone
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_53175.png

Downloads & links

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Map

FileDownload / File: emd_53175.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of mouse TRPM3 alpha 2 in complex with antagonist Primidone
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.7 Å/pix.
x 480 pix.
= 336. Å		0.7 Å/pix.
x 480 pix.
= 336. Å		0.7 Å/pix.
x 480 pix.
= 336. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.7 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.017
Minimum - Maximum-0.046806805 - 0.10427593
Average (Standard dev.)0.00026835335 (±0.0028138333)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 336.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53175_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpened map

Fileemd_53175_additional_1.map
AnnotationSharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: halfB

Fileemd_53175_half_map_1.map
AnnotationhalfB
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: halfA

Fileemd_53175_half_map_2.map
AnnotationhalfA
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 in complex with antago...

EntireName: Tetrameric assembly of mouse TRPM3 alpha 2 in complex with antagonist Primidone
Components
  • Complex: Tetrameric assembly of mouse TRPM3 alpha 2 in complex with antagonist Primidone
    • Protein or peptide: MKIAA1616 protein
  • Ligand: (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en
  • Ligand: primidone
  • Ligand: 1,2-DISTEAROYL-SN-GLYCERO-3-PHOSPHATE

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Supramolecule #1: Tetrameric assembly of mouse TRPM3 alpha 2 in complex with antago...

SupramoleculeName: Tetrameric assembly of mouse TRPM3 alpha 2 in complex with antagonist Primidone
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: MKIAA1616 protein

MacromoleculeName: MKIAA1616 protein / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 161.96325 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSGKKWRDAG ELERGCSDRE DSAESRRRSR SASRGRFAES WKRLSSKQGS TKRSGLPAQQ TPAQKSWIER AFYKRECVHI IPSTKDPHR CCCGRLIGQH VGLTPSISVL QNEKNESRLS RNDIQSEKWS ISKHTQLSPT DAFGTIEFQG GGHSNKAMYV R VSFDTKPD ...String:
MSGKKWRDAG ELERGCSDRE DSAESRRRSR SASRGRFAES WKRLSSKQGS TKRSGLPAQQ TPAQKSWIER AFYKRECVHI IPSTKDPHR CCCGRLIGQH VGLTPSISVL QNEKNESRLS RNDIQSEKWS ISKHTQLSPT DAFGTIEFQG GGHSNKAMYV R VSFDTKPD LLLHLMTKEW QLELPKLLIS VHGGLQNFEL QPKLKQVFGK GLIKAAMTTG AWIFTGGVNT GVIRHVGDAL KD HASKSRG KICTIGIAPW GIVENQEDLI GRDVVRPYQT MSNPMSKLTV LNSMHSHFIL ADNGTTGKYG AEVKLRRQLE KHI SLQKIN TRIGQGVPVV ALIVEGGPNV ISIVLEYLRD TPPVPVVVCD GSGRASDILA FGHKYSEEGG LINESLRDQL LVTI QKTFT YTRTQAQHLF IILMECMKKK ELITVFRMGS EGHQDIDLAI LTALLKGANA SAPDQLSLAL AWNRVDIARS QIFIY GQQW PVGSLEQAML DALVLDRVDF VKLLIENGVS MHRFLTISRL EELYNTRHGP SNTLYHLVRD VKKGNLPPDY RISLID IGL VIEYLMGGAY RCNYTRKRFR TLYHNLFGPK RPKALKLLGM EDDIPLRRGR KTTKKREEEV DIDLDDPEIN HFPFPFH EL MVWAVLMKRQ KMALFFWQHG EEAMAKALVA CKLCKAMAHE ASENDMVDDI SQELNHNSRD FGQLAVELLD QSYKQDEQ L AMKLLTYELK NWSNATCLQL AVAAKHRDFI AHTCSQMLLT DMWMGRLRMR KNSGLKVILG ILLPPSILSL EFKNKDDMP YMTQAQEIHL QEKEPEEPEK PTKEKDEEDM ELTAMLGRSN GESSRKKDEE EVQSRHRLIP VGRKIYEFYN APIVKFWFYT LAYIGYLML FNYIVLVKME RWPSTQEWIV ISYIFTLGIE KMREILMSEP GKLLQKVKVW LQEYWNVTDL IAILLFSVGM I LRLQDQPF RSDGRVIYCV NIIYWYIRLL DIFGVNKYLG PYVMMIGKMM IDMMYFVIIM LVVLMSFGVA RQAILFPNEE PS WKLAKNI FYMPYWMIYG EVFADQIDPP CGQNETREDG KTIQLPPCKT GAWIVPAIMA CYLLVANILL VNLLIAVFNN TFF EVKSIS NQVWKFQRYQ LIMTFHERPV LPPPLIIFSH MTMIFQHVCC RWRKHESDQD ERDYGLKLFI TDDELKKVHD FEEQ CIEEY FREKDDRFNS SNDERIRVTS ERVENMSMRL EEVNEREHSM KASLQTVDIR LAQLEDLIGR MATALERLTG LERAE SNKI RSRTSSDCTD AAYIVRQSSF NSQEGNTFKL QESIDPAGEE TISPTSPTLM PRMRSHSFYS VALEVLFQGP QGTEQK LIS EEDLRGASMD EKTTGWRGGH VVEGLAGELE QLRARLEHHP QGQREP

UniProtKB: Transient receptor potential cation channel subfamily M member 3

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Macromolecule #2: (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]sp...

MacromoleculeName: (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en
type: ligand / ID: 2 / Number of copies: 4 / Formula: 9Z9
Molecular weightTheoretical: 544.805 Da
Chemical component information

ChemComp-9Z9:
(3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en / detergent*YM

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Macromolecule #3: primidone

MacromoleculeName: primidone / type: ligand / ID: 3 / Number of copies: 4 / Formula: A1AIA
Molecular weightTheoretical: 218.252 Da

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Macromolecule #4: 1,2-DISTEAROYL-SN-GLYCERO-3-PHOSPHATE

MacromoleculeName: 1,2-DISTEAROYL-SN-GLYCERO-3-PHOSPHATE / type: ligand / ID: 4 / Number of copies: 4 / Formula: PX8
Molecular weightTheoretical: 703.99 Da
Chemical component information

ChemComp-PX8:
1,2-DISTEAROYL-SN-GLYCERO-3-PHOSPHATE

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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
100.0 uMC12H14N2O2Primidone

Details: 10 mM Hepes pH 7.5, 150 mM NaCl, 0.063% Glycodiosgenin, 100 uM Primidone
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GRAPHENE / Support film - topology: CONTINUOUS
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: 1.2 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: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 76411
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-9qho:
Cryo-EM structure of mouse TRPM3 alpha 2 in complex with antagonist Primidone

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