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

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Basic information

Entry
Database: PDB / ID: 9qho
TitleCryo-EM structure of mouse TRPM3 alpha 2 in complex with antagonist Primidone
ComponentsMKIAA1616 protein
KeywordsMEMBRANE PROTEIN / Ca2+ channel Primidone-bound Closed conformation
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
: / 1,2-DISTEAROYL-SN-GLYCERO-3-PHOSPHATE / Transient receptor potential cation channel subfamily M member 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.28 Å
AuthorsShkumatov, A.V. / Schenck, S. / Brunner, J.D.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of mouse TRPM3 alpha 2 in complex with antagonist Primidone
Authors: Shkumatov, A.V. / Schenck, S. / Brunner, J.D.
History
DepositionMar 16, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 11, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MKIAA1616 protein
B: MKIAA1616 protein
C: MKIAA1616 protein
D: MKIAA1616 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)653,72116
Polymers647,8534
Non-polymers5,86812
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
MKIAA1616 protein


Mass: 161963.250 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Trpm3, mKIAA1616 / Variant: alpha 2 / Plasmid: pcDNA5/TO / Cell line (production host): Flp-In T-REx 293 / Production host: Homo sapiens (human) / References: UniProt: Q69ZE8
#2: Chemical
ChemComp-9Z9 / (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en


Mass: 544.805 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H56O5 / Comment: detergent*YM
#3: Chemical
ChemComp-A1AIA / primidone / 5-ethyl-5-phenyl-1,3-diazinane-4,6-dione


Mass: 218.252 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H14N2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-PX8 / 1,2-DISTEAROYL-SN-GLYCERO-3-PHOSPHATE


Mass: 703.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C39H76O8P
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Tetrameric assembly of mouse TRPM3 alpha 2 in complex with antagonist Primidone
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.161 MDa / Experimental value: NO
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Homo sapiens (human) / Strain: Flp-In T-REx 293
Buffer solutionpH: 7.5
Details: 10 mM Hepes pH 7.5, 150 mM NaCl, 0.063% Glycodiosgenin, 100 uM Primidone
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMHepesC8H17N2NaO4S1
2150 mMSodium chlorideNaCl1
30.0063 %GlycodiosgeninC56H92O251
4100 uMPrimidoneC12H14N2O21
SpecimenConc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 298.15 K

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1200 nm / Nominal defocus min: 700 nm
Image recordingElectron dose: 62 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCv4.4.1particle selection
2SerialEM4.1 beta 26image acquisition
9PHENIX1.21-5207model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 76411 / Symmetry type: POINT
Atomic model buildingSource name: PDB / Type: experimental model
RefinementHighest resolution: 3.28 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00429120
ELECTRON MICROSCOPYf_angle_d0.52339384
ELECTRON MICROSCOPYf_dihedral_angle_d7.7894296
ELECTRON MICROSCOPYf_chiral_restr0.0364384
ELECTRON MICROSCOPYf_plane_restr0.0044884

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