9YVP | pdb_00009yvp

Cryo-EM structure of the L900V;R993P;S1060R mutant mouse TRPM4 channel in an open state bound to NC1 and PI(4,5)P2.

PDB DOI: https://doi.org/10.2210/pdb9YVP/pdb
EM Map EMD-73531: EMDB EMDataResource

Classification: TRANSPORT PROTEIN
Organism(s): Mus musculus
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2025-10-23 Released: 2026-07-01
Deposition Author(s): Teixeira-Duarte, C.M., Jiang, Y.
Funding Organization(s): Howard Hughes Medical Institute (HHMI), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Welch Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.81 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Structural mechanism of Necrocide 1 activation of human TRPM4 that triggers necrosis by sodium overload.

Teixeira-Duarte, C.M., Fu, W., Zeng, W., Wang, J., Jiang, X., Zhao, Z., Zhong, Q., Jiang, Y.

(2026) bioRxiv

PubMed: 41659621 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.64898/2026.01.28.702369
Primary Citation Related Structures:
9YVP

PubMed Abstract:
The small molecule Necrocide 1 (NC1) constitutively activates human TRPM4, triggering Na ⁺ influx and leading to necrotic cell death, a process termed Necrosis by Sodium Overload (NECSO). NC1 activation is specific to human TRPM4 and does not affect most of the other mammalian TRPM4 orthologs. Here, we elucidate the molecular mechanism underlying NC1 activation and its species-specific selectivity for human TRPM4 using a combination of single-particle cryo-EM, electrophysiology, and cell death assays. We identify the NC1-binding site and the key molecular determinants responsible for channel activation. In addition, we explain the insensitivity of mouse TRPM4 to NC1 and pinpoint specific residues that define NC1 specificity for human TRPM4. Given the upregulation of TRPM4 in various human cancers, our mechanistic insights into NC1 activation and specificity provide a framework for the potential development of cancer therapeutics targeting TRPM4-mediated necrosis.

Organizational Affiliation

Howard Hughes Medical Institute and Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA.

Macromolecule Content

Total Structure Weight: 556.43 kDa
Atom Count: 30,036
Modeled Residue Count: 3,732
Deposited Residue Count: 4,916
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transient receptor potential cation channel subfamily M member 4	A [auth B], B [auth A], C, D	1,229	Mus musculus	Mutation(s): 3 Gene Names: Trpm4, Ltrpc4
UniProt
Find proteins for Q7TN37 (Mus musculus) Explore Q7TN37 Go to UniProtKB: Q7TN37
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7TN37
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PT5 (Subject of Investigation/LOI) Query on PT5 Download:Ideal Coordinates CCD File SDF format, chain O [auth D] SDF format, chain L [auth C] SDF format, chain I [auth A] SDF format, chain F [auth B] MOL2 format, chain O [auth D] MOL2 format, chain L [auth C] MOL2 format, chain I [auth A] MOL2 format, chain F [auth B] mmCIF format, chain O [auth D] mmCIF format, chain L [auth C] mmCIF format, chain I [auth A] mmCIF format, chain F [auth B]	F [auth B], I [auth A], L [auth C], O [auth D]	[(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phospho ryl]oxy-propan-2-yl] (8Z)-icosa-5,8,11,14-tetraenoate C₄₇ H₈₅ O₁₉ P₃ CNWINRVXAYPOMW-HJBQCNPJSA-N		Interactions Focus chain F [auth B] Focus chain I [auth A] Focus chain L [auth C] Focus chain O [auth D] Interactions & Density Focus chain F [auth B] Focus chain I [auth A] Focus chain L [auth C] Focus chain O [auth D]
A1CY8 (Subject of Investigation/LOI) Query on A1CY8 Download:Ideal Coordinates CCD File SDF format, chain P [auth D] SDF format, chain M [auth C] SDF format, chain J [auth A] SDF format, chain G [auth B] MOL2 format, chain P [auth D] MOL2 format, chain M [auth C] MOL2 format, chain J [auth A] MOL2 format, chain G [auth B] mmCIF format, chain P [auth D] mmCIF format, chain M [auth C] mmCIF format, chain J [auth A] mmCIF format, chain G [auth B]	G [auth B], J [auth A], M [auth C], P [auth D]	Necrocide 1 C₂₃ H₂₇ N O₃ JLWDEIVDLTXBGE-QHCPKHFHSA-N		Interactions Focus chain G [auth B] Focus chain J [auth A] Focus chain M [auth C] Focus chain P [auth D] Interactions & Density Focus chain G [auth B] Focus chain J [auth A] Focus chain M [auth C] Focus chain P [auth D]
CA (Subject of Investigation/LOI) Query on CA Download:Ideal Coordinates CCD File SDF format, chain N [auth D] SDF format, chain K [auth C] SDF format, chain H [auth A] SDF format, chain E [auth B] MOL2 format, chain N [auth D] MOL2 format, chain K [auth C] MOL2 format, chain H [auth A] MOL2 format, chain E [auth B] mmCIF format, chain N [auth D] mmCIF format, chain K [auth C] mmCIF format, chain H [auth A] mmCIF format, chain E [auth B]	E [auth B], H [auth A], K [auth C], N [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Focus chain H [auth A] Focus chain K [auth C] Focus chain N [auth D] Interactions & Density Focus chain E [auth B] Focus chain H [auth A] Focus chain K [auth C] Focus chain N [auth D]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.81 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419
RECONSTRUCTION	cryoSPARC

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-07-01

Deposition Author(s):

Teixeira-Duarte, C.M.

Jiang, Y.

Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	--
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35 GM140892
Welch Foundation	United States	I-1578