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- EMDB-65116: Cryo-EM structure of TRP melastatin channel in the closed state -

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Basic information

Entry
Database: EMDB / ID: EMD-65116
TitleCryo-EM structure of TRP melastatin channel in the closed state
Map data
Sample
  • Complex: Transient receptor potential cation channel subfamily M member 8
    • Protein or peptide: Transient receptor potential cation channel subfamily M member 8
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
KeywordsTRP / MEMBRANE PROTEIN
Function / homology
Function and homology information


TRP channels / thermoception / ligand-gated calcium channel activity / response to temperature stimulus / plasma membrane raft / monoatomic ion channel activity / response to cold / calcium ion transmembrane transport / calcium channel activity / intracellular calcium ion homeostasis ...TRP channels / thermoception / ligand-gated calcium channel activity / response to temperature stimulus / plasma membrane raft / monoatomic ion channel activity / response to cold / calcium ion transmembrane transport / calcium channel activity / intracellular calcium ion homeostasis / calcium ion transport / positive regulation of cold-induced thermogenesis / membrane raft / external side of plasma membrane / membrane / identical protein binding / plasma membrane
Similarity search - Function
TRPM, SLOG domain / : / : / SLOG in TRPM / TRPM2-like domain / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Transient receptor potential cation channel subfamily M member 8
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.43 Å
AuthorsKim S-H / Park H / Lee HH
Funding support Korea, Republic Of, 1 items
OrganizationGrant numberCountry
Samsung Science and Technology Foundation Korea, Republic Of
CitationJournal: To Be Published
Title: Cryo-EM structure of TRP melastatin channel in the closed state
Authors: Kim S-H / Park H / Lee HH
History
DepositionJun 21, 2025-
Header (metadata) releaseJun 24, 2026-
Map releaseJun 24, 2026-
UpdateJun 24, 2026-
Current statusJun 24, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_65116.png

Downloads & links

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Map

FileDownload / File: emd_65116.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 320 pix.
= 353.6 Å		1.11 Å/pix.
x 320 pix.
= 353.6 Å		1.11 Å/pix.
x 320 pix.
= 353.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.105 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.055
Minimum - Maximum-0.3786193 - 0.615067
Average (Standard dev.)-0.00025818308 (±0.014452128)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 353.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_65116_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_65116_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 : Transient receptor potential cation channel subfamily M member 8

EntireName: Transient receptor potential cation channel subfamily M member 8
Components
  • Complex: Transient receptor potential cation channel subfamily M member 8
    • Protein or peptide: Transient receptor potential cation channel subfamily M member 8
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate

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Supramolecule #1: Transient receptor potential cation channel subfamily M member 8

SupramoleculeName: Transient receptor potential cation channel subfamily M member 8
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 8

MacromoleculeName: Transient receptor potential cation channel subfamily M member 8
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 129.402055 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GPARGIQSFE GARLSMRSRR NGTMGSTRTL YSSVSRSTDV SYSDSDLVNF IQANFKKREC VFFTRDSKAM ENICKCGYAQ SQHIEGTQI NQNEKWNYKK HTKEFPTDAF GDIQFETLGK KGKYLRLSCD TDSETLYELL TQHWHLKTPN LVISVTGGAK N FALKPRMR ...String:
GPARGIQSFE GARLSMRSRR NGTMGSTRTL YSSVSRSTDV SYSDSDLVNF IQANFKKREC VFFTRDSKAM ENICKCGYAQ SQHIEGTQI NQNEKWNYKK HTKEFPTDAF GDIQFETLGK KGKYLRLSCD TDSETLYELL TQHWHLKTPN LVISVTGGAK N FALKPRMR KIFSRLIYIA QSKGAWILTG GTHYGLMKYI GEVVRDNTIS RNSEENIVAI GIAAWGMVSN RDTLIRSCDD EG HFSAQYI MDDFTRDPLY ILDNNHTHLL LVDNGCHGHP TVEAKLRNQL EKYISERTSQ DSNYGGKIPI VCFAQGGGRE TLK AINTSV KSKIPCVVVE GSGQIADVIA SLVEVEDVLT SSMVKEKLVR FLPRTVSRLP EEEIESWIKW LKEILESSHL LTVI KMEEA GDEIVSNAIS YALYKAFSTN EQDKDNWNGQ LKLLLEWNQL DLASDEIFTN DRRWESADLQ EVMFTALIKD RPKFV RLFL ENGLNLQKFL TNEVLTELFS THFSTLVYRN LQIAKNSYND ALLTFVWKLV ANFRRSFWKE DRSSREDLDV ELHDAS LTT RHPLQALFIW AILQNKKELS KVIWEQTKGC TLAALGASKL LKTLAKVKND INAAGESEEL ANEYETRAVE LFTECYS ND EDLAEQLLVY SCEAWGGSNC LELAVEATDQ HFIAQPGVQN FLSKQWYGEI SRDTKNWKII LCLFIIPLVG CGLVSFRK K PIDKHKKLLW YYVAFFTSPF VVFSWNVVFY IAFLLLFAYV LLMDFHSVPH TPELILYALV FVLFCDEVRQ WYMNGVNYF TDLWNVMDTL GLFYFIAGIV FRLHSSNKSS LYSGRVIFCL DYIIFTLRLI HIFTVSRNLG PKIIMLQRML IDVFFFLFLF AVWMVAFGV ARQGILRQNE QRWRWIFRSV IYEPYLAMFG QVPSDVDSTT YDFSHCTFSG NESKPLCVEL DEHNLPRFPE W ITIPLVCI YMLSTNILLV NLLVAMFGYT VGIVQENNDQ VWKFQRYFLV QEYCNRLNIP FPFVVFAYFY MVVKKCFKCC CK EKNMESN ACCFRNEDNE TLAWEGVMKE NYLVKINTKA NDNSEEMRHR FRQLDSKLND LKSLLKEIAN NIKDYKDDDD K

UniProtKB: Transient receptor potential cation channel subfamily M member 8

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Macromolecule #2: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 2 / Number of copies: 12 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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Macromolecule #3: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...

MacromoleculeName: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
type: ligand / ID: 3 / Number of copies: 4 / Formula: POV
Molecular weightTheoretical: 760.076 Da
Chemical component information

ChemComp-POV:
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / phospholipid*YM

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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

Concentration4 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 48.83 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.9 µm

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Image processing

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8e4p

Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.43 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 34033
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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