9VJN | pdb_00009vjn

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

PDB DOI: https://doi.org/10.2210/pdb9VJN/pdb
EM Map EMD-65116: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Mus musculus
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2025-06-21 Released: 2026-06-24
Deposition Author(s): Kim, S.-H., Park, H., Lee, H.H.
Funding Organization(s): Samsung Science and Technology Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.43 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9VJN

This is version 1.0 of the entry. See complete history.

Literature

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

Kim, S.-H., Park, H., Lee, H.H.

To be published.

Macromolecule Content

Total Structure Weight: 526.49 kDa
Atom Count: 28,320
Modeled Residue Count: 3,380
Deposited Residue Count: 4,472
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transient receptor potential cation channel subfamily M member 8	A, B [auth D], C, D [auth B]	1,118	Mus musculus	Mutation(s): 0 Gene Names: Trpm8, Ltrpc6, Trpp8
UniProt
Find proteins for Q8R4D5 (Mus musculus) Explore Q8R4D5 Go to UniProtKB: Q8R4D5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8R4D5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
POV (Subject of Investigation/LOI) Query on POV Download:Ideal Coordinates CCD File SDF format, chain T [auth B] SDF format, chain P [auth C] SDF format, chain L [auth D] SDF format, chain H [auth A] MOL2 format, chain T [auth B] MOL2 format, chain P [auth C] MOL2 format, chain L [auth D] MOL2 format, chain H [auth A] mmCIF format, chain T [auth B] mmCIF format, chain P [auth C] mmCIF format, chain L [auth D] mmCIF format, chain H [auth A]	H [auth A], L [auth D], P [auth C], T [auth B]	(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate C₄₂ H₈₂ N O₈ P WTJKGGKOPKCXLL-PFDVCBLKSA-N		Interactions Focus chain H [auth A] Focus chain L [auth D] Focus chain P [auth C] Focus chain T [auth B] Interactions & Density Focus chain H [auth A] Focus chain L [auth D] Focus chain P [auth C] Focus chain T [auth B]
Y01 (Subject of Investigation/LOI) Query on Y01 Download:Ideal Coordinates CCD File SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain O [auth C] SDF format, chain N [auth C] SDF format, chain M [auth C] SDF format, chain K [auth D] SDF format, chain J [auth D] SDF format, chain I [auth D] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain O [auth C] MOL2 format, chain N [auth C] MOL2 format, chain M [auth C] MOL2 format, chain K [auth D] MOL2 format, chain J [auth D] MOL2 format, chain I [auth D] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain O [auth C] mmCIF format, chain N [auth C] mmCIF format, chain M [auth C] mmCIF format, chain K [auth D] mmCIF format, chain J [auth D] mmCIF format, chain I [auth D] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth A] I [auth D] J [auth D] E [auth A], F [auth A], G [auth A], I [auth D], J [auth D], K [auth D], M [auth C], N [auth C], O [auth C], Q [auth B], R [auth B], S [auth B]	CHOLESTEROL HEMISUCCINATE C₃₁ H₅₀ O₄ WLNARFZDISHUGS-MIXBDBMTSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth D] Focus chain J [auth D] Focus chain K [auth D] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth D] Focus chain J [auth D] Focus chain K [auth D] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.43 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-06-24

Deposition Author(s):

Funding Organization	Location	Grant Number
Samsung Science and Technology Foundation	Korea, Republic Of	--

Revision History (Full details and data files)

Version 1.0: 2026-06-24
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.