9QHQ | pdb_00009qhq

Cryo-EM structure of mouse TRPM3 alpha 2 in with agonists CIM-0216 and Pregnenolone sulfate (PregS)

PDB DOI: https://doi.org/10.2210/pdb9QHQ/pdb
EM Map EMD-53177: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Mus musculus
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2025-03-16 Released: 2026-02-11
Deposition Author(s): Shkumatov, A.V., Schenck, S., Brunner, J.D.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.07 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history.

Literature

Cryo-EM structure of mouse TRPM3 alpha 2 in complex with agonists CIM-0216 and Pregnenolone sulfate (PregS)

Shkumatov, A.V., Schenck, S., Brunner, J.D.

To be published.

Macromolecule Content

Total Structure Weight: 652.38 kDa
Atom Count: 31,308
Modeled Residue Count: 3,824
Deposited Residue Count: 5,636
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MKIAA1616 protein	A, B, C, D	1,409	Mus musculus	Mutation(s): 0 Gene Names: Trpm3, mKIAA1616
UniProt & NIH Common Fund Data Resources
Find proteins for Q69ZE8 (Mus musculus) Explore Q69ZE8 Go to UniProtKB: Q69ZE8
IMPC: MGI:2443101
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q69ZE8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A8W (Subject of Investigation/LOI) Query on A8W Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain M [auth C] SDF format, chain O [auth D] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain M [auth C] MOL2 format, chain O [auth D] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain M [auth C] mmCIF format, chain O [auth D]	F [auth A], I [auth B], M [auth C], O [auth D]	Pregnenolone sulfate C₂₁ H₃₂ O₅ S DIJBBUIOWGGQOP-QGVNFLHTSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain O [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain O [auth D]
CLR Query on CLR Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain K [auth C] SDF format, chain N [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain K [auth C] MOL2 format, chain N [auth D] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain K [auth C] mmCIF format, chain N [auth D]	G [auth A], H [auth A], K [auth C], N [auth D]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth C] Focus chain N [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth C] Focus chain N [auth D]
A1I8P (Subject of Investigation/LOI) Query on A1I8P Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth B] SDF format, chain L [auth C] SDF format, chain P [auth D] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C] MOL2 format, chain P [auth D] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain L [auth C] mmCIF format, chain P [auth D]	E [auth A], J [auth B], L [auth C], P [auth D]	(2~{R})-2-(3,4-dihydro-2~{H}-quinolin-1-yl)-~{N}-(5-methyl-1,2-oxazol-3-yl)-2-phenyl-ethanamide C₂₁ H₂₁ N₃ O₂ KSEXDSJYVSEVGF-HXUWFJFHSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain P [auth D] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain P [auth D]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.07 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21-5207

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-02-11

Deposition Author(s):

Shkumatov, A.V.

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2026-02-11
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.