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- EMDB-73529: Cryo-EM structure of the mouse TRPM4 channel bound to NC1. -

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Basic information

Entry
Database: EMDB / ID: EMD-73529
TitleCryo-EM structure of the mouse TRPM4 channel bound to NC1.
Map data
Sample
  • Complex: mouse TRPM4
    • Protein or peptide: Transient receptor potential cation channel subfamily M member 4
  • Ligand: Necrocide 1
KeywordsTRPM4 / Ion channel / TRANSPORT PROTEIN
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.42 Å
AuthorsTeixeira-Duarte CM / Jiang Y
Funding support United States, 3 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM140892 United States
Welch FoundationI-1578 United States
CitationJournal: Nat Commun / Year: 2026
Title: Structural mechanism of Necrocide 1 activation of human TRPM4 that triggers necrosis by sodium overload
Authors: Teixeira-Duarte CM / Fu W / Zeng W / Wang J / Jiang X / Zhao Z / Zhong Q / Jiang Y
History
DepositionOct 23, 2025-
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73529.png

Downloads & links

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Map

FileDownload / File: emd_73529.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 360 pix.
= 264.546 Å		0.73 Å/pix.
x 360 pix.
= 264.546 Å		0.73 Å/pix.
x 360 pix.
= 264.546 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.73485 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.41367882 - 0.55914515
Average (Standard dev.)0.003025603 (±0.017428238)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 264.546 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_73529_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_73529_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : mouse TRPM4

EntireName: mouse TRPM4
Components
  • Complex: mouse TRPM4
    • Protein or peptide: Transient receptor potential cation channel subfamily M member 4
  • Ligand: Necrocide 1

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Supramolecule #1: mouse TRPM4

SupramoleculeName: mouse TRPM4 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Transient receptor potential cation channel subfamily M member 4

MacromoleculeName: Transient receptor potential cation channel subfamily M member 4
type: protein_or_peptide / ID: 1 / Details: C terminal thrombin cleavage site and FLAG tag. / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 137.658391 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MVGPEKEQSW IPKIFRKKVC TTFIVDLSDD AGGTLCQCGQ PRDAHPSVAV EDAFGAAVVT EWNSDEHTTE KPTDAYGDLD FTYSGRKHS NFLRLSDRTD PATVYSLVTR SWGFRAPNLV VSVLGGSGGP VLQTWLQDLL RRGLVRAAQS TGAWIVTGGL H TGIGRHVG ...String:
MVGPEKEQSW IPKIFRKKVC TTFIVDLSDD AGGTLCQCGQ PRDAHPSVAV EDAFGAAVVT EWNSDEHTTE KPTDAYGDLD FTYSGRKHS NFLRLSDRTD PATVYSLVTR SWGFRAPNLV VSVLGGSGGP VLQTWLQDLL RRGLVRAAQS TGAWIVTGGL H TGIGRHVG VAVRDHQTAS TGSSKVVAMG VAPWGVVRNR DMLINPKGSF PARYRWRGDP EDGVEFPLDY NYSAFFLVDD GT YGRLGGE NRFRLRFESY VAQQKTGVGG TGIDIPVLLL LIDGDEKMLK RIEDATQAQL PCLLVAGSGG AADCLVETLE DTL APGSGG LRRGEARDRI RRYFPKGDPE VLQAQVERIM TRKELLTVYS SEDGSEEFET IVLRALVKAC GSSEASAYLD ELRL AVAWN RVDIAQSELF RGDIQWRSFH LEASLMDALL NDRPEFVRLL ISHGLSLGHF LTPVRLAQLY SAVSPNSLIR NLLDQ ASHA SSSKSPPVNG TVELRPPNVG QVLRTLLGET CAPRYPARNT RDSYLGQDHR ENDSLLMDWA NKQPSTDASF EQAPWS DLL IWALLLNRAQ MAIYFWEKGS NSVASALGAC LLLRVMARLE SEAEEAARRK DLAATFESMS VDLFGECYHN SEERAAR LL LRRCPLWGEA TCLQLAMQAD ARAFFAQDGV QSLLTQKWWG EMDSTTPIWA LLLAFFCPPL IYTNLIVFRK SEEEPTQK D LDFDMDSSIN GAGPPGTVEP SAKVALERRQ RRRPGRALCC GKFSKRWSDF WGAPVTAFLG NVVSYLLFLL LFAHVLLVD FQPTKPSVSE LLLYFWAFTL LCEELRQGLG GGWGSLASGG RGPDRAPLRH RLHLYLSDTW NQCDLLALTC FLLGVGCRLT PGLFDLGRT VLCLDFMIFT LRLLHIFTVN KQLGPKIVIV SKMMKDVFFF LFFLCVWLVA YGVATEGILR PQDRSLPSIL R RVFYRPYL QIFGQIPQEE MDVALMIPGN CSMERGSWAH PEGPVAGSCV SQYANWLVVL LLIVFLLVAN ILLLNLLIAM FS YTFSKVH GNSDLYWKAQ RYSLIREFHS RPALAPPLII ISHVRLLIKW LRRCRRCRRA NLPASPVFEH FRVCLSKEAE RKL LTWESV HKENFLLAQA RDKRDSDSER LKRTSQKVDT ALKQLGQIRE YDRRLRGLER EVQHCSRVLT WMAEALSHSA LLPP GAPPP PSPTGSKDLV PRGSGADYKD DDDK

UniProtKB: Transient receptor potential cation channel subfamily M member 4

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Macromolecule #2: Necrocide 1

MacromoleculeName: Necrocide 1 / type: ligand / ID: 2 / Number of copies: 4 / Formula: A1CY8
Molecular weightTheoretical: 365.465 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.9 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6bcj

Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.42 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 28221
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

SoftwareName: Coot (ver. 1.1.18)
Output model

PDB-9yvn:
Cryo-EM structure of the mouse TRPM4 channel bound to NC1.

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