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- EMDB-65120: Cryo-EM structure of TRP melastatin channel with icilin -

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Basic information

Entry
Database: EMDB / ID: EMD-65120
TitleCryo-EM structure of TRP melastatin channel with icilin
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: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate
  • Ligand: CALCIUM ION
  • Ligand: Icilin
  • Ligand: CHOLESTEROL
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: 3.1 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 with icilin
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_65120.png

Downloads & links

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Map

FileDownload / File: emd_65120.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 300 pix.
= 315. Å		1.05 Å/pix.
x 300 pix.
= 315. Å		1.05 Å/pix.
x 300 pix.
= 315. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.155
Minimum - Maximum-0.8975348 - 1.398484
Average (Standard dev.)-0.0004441885 (±0.04256263)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 315.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_65120_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_65120_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: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate
  • Ligand: CALCIUM ION
  • Ligand: Icilin
  • Ligand: CHOLESTEROL

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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: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(o...

MacromoleculeName: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate
type: ligand / ID: 2 / Number of copies: 4 / Formula: PIO
Molecular weightTheoretical: 746.566 Da
Chemical component information

ChemComp-PIO:
[(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate

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Macromolecule #3: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 3 / Number of copies: 4 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #4: Icilin

MacromoleculeName: Icilin / type: ligand / ID: 4 / Number of copies: 4 / Formula: KX7
Molecular weightTheoretical: 311.292 Da
Chemical component information

ChemComp-KX7:
Icilin / agonist*YM

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Macromolecule #5: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 5 / Number of copies: 4 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

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

8e4o

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 41143
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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