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- PDB-9qhq: Cryo-EM structure of mouse TRPM3 alpha 2 in with agonists CIM-021... -

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Basic information

Entry
Database: PDB / ID: 9qhq
TitleCryo-EM structure of mouse TRPM3 alpha 2 in with agonists CIM-0216 and Pregnenolone sulfate (PregS)
ComponentsMKIAA1616 protein
KeywordsMEMBRANE PROTEIN / Ca2+ channel CIM-0216-bound Pregnenolone sulfate-bound
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
: / Pregnenolone sulfate / CHOLESTEROL / 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: 3.07 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 agonists CIM-0216 and Pregnenolone sulfate (PregS)
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

Downloads & links

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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)652,37516
Polymers647,8534
Non-polymers4,52212
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-A1I8P / (2~{R})-2-(3,4-dihydro-2~{H}-quinolin-1-yl)-~{N}-(5-methyl-1,2-oxazol-3-yl)-2-phenyl-ethanamide


Mass: 347.410 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H21N3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-A8W / Pregnenolone sulfate / pregn-5-en-3beta-ol-20-one-3beta-sulfate


Mass: 396.541 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H32O5S / Feature type: SUBJECT OF INVESTIGATION / Comment: antidepressant*YM
#4: Chemical
ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H46O
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 with CIM-0216 and neurosteroid Pregnenolone sulfate (PregS)
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, 100um PI(4,5)P2, 10 uM CIM-0216, 250 uM Pregnenolone sulfate
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMHepesC8H17N2NaO4S1
2150 mMSodium chlorideNaCl1
30.0063 %GlycodiosgeninC56H92O251
4100 uML-alpha-phosphatidylinositol-4,5-bisphosphate1
510 uMCIM-0216C21H21N3O21
6250 uMPregnenolone sulfateC21H32O5S1
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 R2/1
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 298.15 K / Details: GP2

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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: 600 nm
Image recordingElectron dose: 62 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCv4.4.1+240110particle selection
2SerialEM4.1.8image acquisition
9PHENIX1.21-5207model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 58787 / Symmetry type: POINT
RefinementHighest resolution: 3.07 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00332052
ELECTRON MICROSCOPYf_angle_d0.53743404
ELECTRON MICROSCOPYf_dihedral_angle_d4.6874504
ELECTRON MICROSCOPYf_chiral_restr0.0374860
ELECTRON MICROSCOPYf_plane_restr0.0045396

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