8RCR | pdb_00008rcr

human TRPM4 in SMA apo

PDB DOI: https://doi.org/10.2210/pdb8RCR/pdb
EM Map EMD-19057: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No
Membrane Protein: Yes PDBTM MemProtMD

Deposited: 2023-12-07 Released: 2024-12-18
Deposition Author(s): Ekundayo, B., Prakash, A., Christian, G., Anne, F.H., Sabrina, G., Mey, B., Daniela, R., Martin, L., Jean, S.R., Henning, S., Hugues, A., Dongchun, N.
Funding Organization(s): Swiss National Science Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Identification of a binding site for small molecule inhibitors targeting human TRPM4.

Ekundayo, B., Arullampalam, P., Gerber, C.E., Hammerli, A.F., Guichard, S., Boukenna, M., Ross-Kaschitza, D., Lochner, M., Rougier, J.S., Stahlberg, H., Abriel, H., Ni, D.

(2025) Nat Commun 16: 833-833

PubMed: 39828793 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-025-56131-2
Primary Citation Related Structures:
8RCR, 8RCU, 8RD9

PubMed Abstract:
Transient receptor potential (TRP) melastatin 4 (TRPM4) protein is a calcium-activated monovalent cation channel associated with various genetic and cardiovascular disorders. The anthranilic acid derivative NBA is a potent and specific TRPM4 inhibitor, but its binding site in TRPM4 has been unknown, although this information is crucial for drug development targeting TRPM4. We determine three cryo-EM structures of full-length human TRPM4 embedded in native lipid nanodiscs without inhibitor, bound to NBA, and an anthranilic acid derivative, IBA. We found that the small molecules NBA and IBA were bound in a pocket formed between the S3, S4, and TRP helices and the S4-S5 linker of TRPM4. Our structural data and results from patch clamp experiments enable validation of a binding site for small molecule inhibitors, paving the way for further drug development targeting TRPM4.

Organizational Affiliation

Laboratory of Biological Electron Microscopy, IPHYS, SB, EPFL, and Dept. Fundamental Microbiology, Faculty of Biology and Medicine, UNIL, Cubotron, Rt. de la Sorge, Lausanne, Switzerland.

Macromolecule Content

Total Structure Weight: 340.01 kDa
Atom Count: 19,936
Modeled Residue Count: 2,420
Deposited Residue Count: 2,992
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, B, C, D	748	Homo sapiens	Mutation(s): 0 Gene Names: TRPM4 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TD43 (Homo sapiens) Explore Q8TD43 Go to UniProtKB: Q8TD43
PHAROS: Q8TD43 GTEx: ENSG00000130529
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8TD43
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CLR Query on CLR Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth C] SDF format, chain N [auth C] SDF format, chain P [auth D] SDF format, chain O [auth D] SDF format, chain M [auth C] SDF format, chain K [auth C] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain L [auth C] MOL2 format, chain N [auth C] MOL2 format, chain P [auth D] MOL2 format, chain O [auth D] MOL2 format, chain M [auth C] MOL2 format, chain K [auth C] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain L [auth C] mmCIF format, chain N [auth C] mmCIF format, chain P [auth D] mmCIF format, chain O [auth D] mmCIF format, chain M [auth C] mmCIF format, chain K [auth C] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth A] H [auth B] I [auth B] E [auth A], F [auth A], G [auth A], H [auth B], I [auth B], J [auth B], K [auth C], L [auth C], M [auth C], N [auth C], O [auth D], P [auth D]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth D] Focus chain P [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth D] Focus chain P [auth D]