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Basic information

Entry
Database: EMDB / ID: EMD-65204
TitleCryo-EM structure of TRP melastatin channel in the intermediate 3 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: [(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
KeywordsTRP / MEMBRANE PROTEIN
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.48 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 intermediate 3 state
Authors: Kim S-H / Park H / Lee HH
History
DepositionJun 30, 2025-
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_65204.png

Downloads & links

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Map

FileReleased
Voxel sizeX=Y=Z: 0.664 Å
Density
Contour LevelBy AUTHOR: 0.024
Minimum - Maximum-0.14316235 - 0.2468597
Average (Standard dev.)0.0008488423 (±0.008023164)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 254.97598 Å
α=β=γ: 90.0 °

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Supplemental data

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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

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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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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: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 69.9 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.7000000000000001 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: 3.48 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 31569
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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