9B29 | pdb_00009b29

Cryo-EM structure of the mouse TRPM3 alpha 2 channel in complex with cholesteryl hemisuccinate


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.13 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9B29

This is version 1.2 of the entry. See complete history

Literature

Molecular basis of neurosteroid and anticonvulsant regulation of TRPM3.

Yin, Y.Park, C.G.Feng, S.Guan, Z.Lee, H.J.Zhang, F.Sharma, K.Borgnia, M.J.Im, W.Lee, S.Y.

(2025) Nat Struct Mol Biol 32: 828-840

  • DOI: https://doi.org/10.1038/s41594-024-01463-8
  • Primary Citation Related Structures: 
    9B28, 9B29, 9B2A

  • PubMed Abstract: 

    Transient receptor potential channel subfamily M member 3 (TRPM3) is a Ca 2+ -permeable cation channel activated by the neurosteroid pregnenolone sulfate (PregS) or heat, serving as a nociceptor in the peripheral sensory system. Recent discoveries of autosomal dominant neurodevelopmental disorders caused by gain-of-function mutations in TRPM3 highlight its role in the central nervous system. Notably, the TRPM3 inhibitor primidone, an anticonvulsant, has proven effective in treating patients with TRPM3-linked neurological disorders and in mouse models of thermal nociception. However, our understanding of neurosteroids, inhibitors and disease mutations on TRPM3 is limited. Here we present cryogenic electron microscopy structures of the mouse TRPM3 in complex with cholesteryl hemisuccinate, primidone and PregS with the synthetic agonist CIM 0216. Our studies identify the binding sites for the neurosteroid, synthetic agonist and inhibitor and offer insights into their effects and disease mutations on TRPM3 gating, aiding future drug development.


  • Organizational Affiliation
    • Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA.

Macromolecule Content 

  • Total Structure Weight: 806.65 kDa 
  • Atom Count: 23,036 
  • Modeled Residue Count: 3,192 
  • Deposited Residue Count: 6,956 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Transient receptor potential cation channel, subfamily M, member 3
A, B, C, D
1,739Mus musculusMutation(s): 0 
Gene Names: Trpm3
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for J9SQF3 (Mus musculus)
Explore J9SQF3 
Go to UniProtKB:  J9SQF3
IMPC:  MGI:2443101
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupJ9SQF3
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LBN

Query on LBN



Download:Ideal Coordinates CCD File
F [auth A],
K [auth B],
P [auth C],
U [auth D]
1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
C42 H82 N O8 P
WTJKGGKOPKCXLL-VYOBOKEXSA-N
6OU

Query on 6OU



Download:Ideal Coordinates CCD File
E [auth A],
J [auth B],
O [auth C],
T [auth D]
[(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate
C39 H76 N O8 P
FHQVHHIBKUMWTI-OTMQOFQLSA-N
PX2

Query on PX2



Download:Ideal Coordinates CCD File
I [auth A],
N [auth B],
S [auth C],
X [auth D]
1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE
C27 H52 O8 P
OKLASJZQBDJAPH-RUZDIDTESA-M
Y01

Query on Y01



Download:Ideal Coordinates CCD File
G [auth A]
H [auth A]
L [auth B]
M [auth B]
Q [auth C]
G [auth A],
H [auth A],
L [auth B],
M [auth B],
Q [auth C],
R [auth C],
V [auth D],
W [auth D]
CHOLESTEROL HEMISUCCINATE
C31 H50 O4
WLNARFZDISHUGS-MIXBDBMTSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.13 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-22
    Type: Initial release
  • Version 1.1: 2025-01-29
    Changes: Data collection, Database references
  • Version 1.2: 2025-05-28
    Changes: Data collection, Database references