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- PDB-9vjn: Cryo-EM structure of TRP melastatin channel in the closed state -

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Basic information

Entry
Database: PDB / ID: 9vjn
TitleCryo-EM structure of TRP melastatin channel in the closed state
ComponentsTransient receptor potential cation channel subfamily M member 8
KeywordsMEMBRANE PROTEIN / TRP
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
Chem-POV / CHOLESTEROL HEMISUCCINATE / Transient receptor potential cation channel subfamily M member 8
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.43 Å
AuthorsKim, S.-H. / Park, H. / Lee, H.H.
Funding support Korea, Republic Of, 1items
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, H.H.
History
DepositionJun 21, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 24, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transient receptor potential cation channel subfamily M member 8
D: Transient receptor potential cation channel subfamily M member 8
C: Transient receptor potential cation channel subfamily M member 8
B: Transient receptor potential cation channel subfamily M member 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)526,48920
Polymers517,6084
Non-polymers8,88116
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Transient receptor potential cation channel subfamily M member 8 / Long transient receptor potential channel 6 / LTrpC-6 / LTrpC6 / Transient receptor potential p8 / Trp-p8


Mass: 129402.055 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Trpm8, Ltrpc6, Trpp8 / Production host: Homo sapiens (human) / References: UniProt: Q8R4D5
#2: Chemical
ChemComp-Y01 / CHOLESTEROL HEMISUCCINATE


Mass: 486.726 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C31H50O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-POV / (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / POPC


Mass: 760.076 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C42H82NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Transient receptor potential cation channel subfamily M member 8
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenConc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal defocus max: 2400 nm / Nominal defocus min: 900 nm
Image recordingElectron dose: 48.83 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2PHENIXmodel refinement
13cryoSPARC3D reconstruction
CTF correctionType: NONE
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 3.43 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 34033 / Symmetry type: POINT
RefinementHighest resolution: 3.43 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00328976
ELECTRON MICROSCOPYf_angle_d0.48139252
ELECTRON MICROSCOPYf_dihedral_angle_d8.7284680
ELECTRON MICROSCOPYf_chiral_restr0.0344444
ELECTRON MICROSCOPYf_plane_restr0.0034756

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