9SMK | pdb_00009smk

Human TRPM4 ion channel in MSP2N2 lipid nanodisc in a calcium-bound state

PDB DOI: https://doi.org/10.2210/pdb9SMK/pdb
EM Map EMD-55036: EMDB EMDataResource

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

Deposited: 2025-09-08 Released: 2026-02-25
Deposition Author(s): Pugh, C.F., Feilen, L.P., Zivkovic, D., Praestegaard, K.F., Sideris, C., Borthwick, N.J., de Lichtenberg, C., Bolla, J.R., Autzen, A.A.A., Autzen, H.E.
Funding Organization(s): Novo Nordisk Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.80 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

MAASTY: a (dis)ordered copolymer for structural determination of human membrane proteins in native nanodiscs.

Pugh, C.F., Feilen, L.P., Zivkovic, D., Praestegaard, K.F., Sideris, C., Borthwick, N.J., de Lichtenberg, C., Bolla, J.R., Autzen, A.A.A., Autzen, H.E.

(2025) Nat Commun 16: 11399-11399

PubMed: 41372170 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41467-025-66208-7
Primary Citation of Related Structures:
9I3R, 9SMK

PubMed Abstract:
Amphiphilic copolymers capable of extracting membrane proteins directly from cellular membranes into "native nanodiscs" offer a simplified approach for preparing membrane proteins in lipid nanodiscs compared to approaches that rely on detergent. Copolymer amphiphilicity, length, and composition influence their performance, in addition to the protein itself and the purification conditions used. Here, we report a copolymer composed of methacrylic acid and styrene, which we term MAASTY, leveraging the inherent monomer reactivity ratios to create an anionic copolymer with a statistical distribution of monomers. We show that MAASTY can be used for high-resolution structural determination of a human membrane protein by single particle cryo-electron microscopy, preserving endogenous lipids including cholesterol and exhibiting an enrichment of phosphatidylinositol. Moreover, MAASTY copolymers effectively solubilize a broad range of lipid species and a wide range of different, eukaryotic membrane proteins from mammalian cells. We find that MAASTY copolymers are promising as effective solubilizers of membrane proteins and offer a chemical platform for structural and functional characterization of membrane proteins in native nanodiscs.

Organizational Affiliation

Department of Biomedical Sciences, University of Copenhagen, Copenhagen, N, DK-2200, Denmark.

Macromolecule Content

Total Structure Weight: 545.08 kDa
Atom Count: 29,716
Modeled Residue Count: 3,728
Deposited Residue Count: 4,872
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 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	1,218	Homo sapiens	Mutation(s): 0 Gene Names: TRPM4, LTRPC4
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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8TD43
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
Y01 Query on Y01 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth C] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain Q [auth D] SDF format, chain S [auth D] SDF format, chain T [auth D] SDF format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth C] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain S [auth D] MOL2 format, chain T [auth D] MOL2 format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth C] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain S [auth D] mmCIF format, chain T [auth D] mmCIF format, chain G [auth A]	F [auth A] G [auth A] H [auth A] J [auth B] K [auth B] F [auth A], G [auth A], H [auth A], J [auth B], K [auth B], L [auth B], M [auth C], O [auth C], P [auth C], Q [auth D], S [auth D], T [auth D]	CHOLESTEROL HEMISUCCINATE C₃₁ H₅₀ O₄ WLNARFZDISHUGS-MIXBDBMTSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth D] Focus chain S [auth D] Focus chain T [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth D] Focus chain S [auth D] Focus chain T [auth D]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain N [auth C] SDF format, chain R [auth D] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain N [auth C] MOL2 format, chain R [auth D] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain N [auth C] mmCIF format, chain R [auth D]	E [auth A], I [auth B], N [auth C], R [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain N [auth C] Focus chain R [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain N [auth C] Focus chain R [auth D]