[English] 日本語
Yorodumi
- EMDB-73528: Cryo-EM structure of the human TRPM4 channel in an open state bou... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-73528
TitleCryo-EM structure of the human TRPM4 channel in an open state bound to NC1 and PI(4,5)P2 in the presence of EGTA.
Map data
Sample
  • Complex: human TRPM4
    • Protein or peptide: Transient receptor potential cation channel subfamily M member 4
  • Ligand: [(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
  • Ligand: Necrocide 1
KeywordsTRPM4 / Ion channel / TRANSPORT PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.73 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

-
Structure visualization

Supplemental images

emd_73528.png

Downloads & links

-
Map

FileDownload / File: emd_73528.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.)
0.86 Å/pix.
x 360 pix.
= 308.52 Å		0.86 Å/pix.
x 360 pix.
= 308.52 Å		0.86 Å/pix.
x 360 pix.
= 308.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.857 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.266
Minimum - Maximum-1.5352536 - 2.055318
Average (Standard dev.)0.0055353697 (±0.058026288)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 308.52 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_73528_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_73528_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : human TRPM4

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

-
Supramolecule #1: human TRPM4

SupramoleculeName: human TRPM4 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

-
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: N terminal FLAG tag and thrombin cleavage site / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 136.265359 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYKDDDDKG SGLVPRGSVV PEKEQSWIPK IFKKKTCTTF IVDSTDPGGT LCQCGRPRTA HPAVAMEDAF GAAVVTVWDS DAHTTEKPT DAYGELDFTG AGRKHSNFLR LSDRTDPAAV YSLVTRTWGF RAPNLVVSVL GGSGGPVLQT WLQDLLRRGL V RAAQSTGA ...String:
MDYKDDDDKG SGLVPRGSVV PEKEQSWIPK IFKKKTCTTF IVDSTDPGGT LCQCGRPRTA HPAVAMEDAF GAAVVTVWDS DAHTTEKPT DAYGELDFTG AGRKHSNFLR LSDRTDPAAV YSLVTRTWGF RAPNLVVSVL GGSGGPVLQT WLQDLLRRGL V RAAQSTGA WIVTGGLHTG IGRHVGVAVR DHQMASTGGT KVVAMGVAPW GVVRNRDTLI NPKGSFPARY RWRGDPEDGV QF PLDYNYS AFFLVDDGTH GCLGGENRFR LRLESYISQQ KTGVGGTGID IPVLLLLIDG DEKMLTRIEN ATQAQLPCLL VAG SGGAAD CLAETLEDTL APGSGGARQG EARDRIRRFF PKGDLEVLQA QVERIMTRKE LLTVYSSEDG SEEFETIVLK ALVK ACGSS EASAYLDELR LAVAWNRVDI AQSELFRGDI QWRSFHLEAS LMDALLNDRP EFVRLLISHG LSLGHFLTPM RLAQL YSAA PSNSLIRNLL DQASHSAGTK APALKGGAAE LRPPDVGHVL RMLLGKMCAP RYPSGGAWDP HPGQGFGESM YLLSDK ATS PLSLDAGLGQ APWSDLLLWA LLLNRAQMAM YFWEMGSNAV SSALGACLLL RVMARLEPDA EEAARRKDLA FKFEGMG VD LFGECYRSSE VRAARLLLRR CPLWGDATCL QLAMQADARA FFAQDGVQSL LTQKWWGDMA STTPIWALVL AFFCPPLI Y TRLITFRKSE EEPTREELEF DMDSVINGEG PVGTADPAEK TPLGVPRQSG RPGCCGGRCG GRRCLRRWFH FWGAPVTIF MGNVVSYLLF LLLFSRVLLV DFQPAPPGSL ELLLYFWAFT LLCEELRQGL SGGGGSLASG GPGPGHASLS QRLRLYLADS WNQCDLVAL TCFLLGVGCR LTPGLYHLGR TVLCIDFMVF TVRLLHIFTV NKQLGPKIVI VSKMMKDVFF FLFFLGVWLV A YGVATEGL LRPRDSDFPS ILRRVFYRPY LQIFGQIPQE DMDVALMEHS NCSSEPGFWA HPPGAQAGTC VSQYANWLVV LL LVIFLLV ANILLVNLLI AMFSYTFGKV QGNSDLYWKA QRYRLIREFH SRPALAPPFI VISHLRLLLR QLCRRPRSPQ PSS PALEHF RVYLSKEAER KLLTWESVHK ENFLLARARD KRESDSERLK RTSQKVDLAL KQLGHIREYE QRLKVLEREV QQCS RVLGW VAEALSRSAL LPPGGPPPPD LPGSKD

UniProtKB: Transient receptor potential cation channel subfamily M member 4

-
Macromolecule #2: [(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tr...

MacromoleculeName: [(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
type: ligand / ID: 2 / Number of copies: 4 / Formula: PT5
Molecular weightTheoretical: 1.047088 KDa

-
Macromolecule #3: Necrocide 1

MacromoleculeName: Necrocide 1 / type: ligand / ID: 3 / Number of copies: 4 / Formula: A1CY8
Molecular weightTheoretical: 365.465 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

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

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k 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

+
Image processing

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

9mrt

Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.73 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 79688
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

-
Atomic model buiding 1

SoftwareName: Coot (ver. 1.1.18)
Output model

PDB-9yvm:
Cryo-EM structure of the human TRPM4 channel in an open state bound to NC1 and PI(4,5)P2 in the presence of EGTA.

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more