9VNC | pdb_00009vnc

Cryo-EM structure of TRP melastatin channel in the desensitized state, with icilin

PDB DOI: https://doi.org/10.2210/pdb9VNC/pdb
EM Map EMD-65207: EMDB EMDataResource

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

Deposited: 2025-06-30 Released: 2026-07-01
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: 3.45 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9VNC

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

Literature

Cryo-EM structure of TRP melastatin channel in the desensitized state, with icilin

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

To be published.

Macromolecule Content

Total Structure Weight: 520.56 kDa
Atom Count: 28,300
Modeled Residue Count: 3,492
Deposited Residue Count: 4,472
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CLR Query on CLR Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain K [auth C] SDF format, chain N [auth B] SDF format, chain H [auth D] MOL2 format, chain G [auth A] MOL2 format, chain K [auth C] MOL2 format, chain N [auth B] MOL2 format, chain H [auth D] mmCIF format, chain G [auth A] mmCIF format, chain K [auth C] mmCIF format, chain N [auth B] mmCIF format, chain H [auth D]	G [auth A], H [auth D], K [auth C], N [auth B]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain G [auth A] Focus chain H [auth D] Focus chain K [auth C] Focus chain N [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth D] Focus chain K [auth C] Focus chain N [auth B]
KX7 (Subject of Investigation/LOI) Query on KX7 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain M [auth C] SDF format, chain P [auth B] SDF format, chain J [auth D] MOL2 format, chain F [auth A] MOL2 format, chain M [auth C] MOL2 format, chain P [auth B] MOL2 format, chain J [auth D] mmCIF format, chain F [auth A] mmCIF format, chain M [auth C] mmCIF format, chain P [auth B] mmCIF format, chain J [auth D]	F [auth A], J [auth D], M [auth C], P [auth B]	Icilin C₁₆ H₁₃ N₃ O₄ RCEFMOGVOYEGJN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth D] Focus chain M [auth C] Focus chain P [auth B] Interactions & Density Focus chain F [auth A] Focus chain J [auth D] Focus chain M [auth C] Focus chain P [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth D] SDF format, chain L [auth C] SDF format, chain O [auth B] MOL2 format, chain E [auth A] MOL2 format, chain I [auth D] MOL2 format, chain L [auth C] MOL2 format, chain O [auth B] mmCIF format, chain E [auth A] mmCIF format, chain I [auth D] mmCIF format, chain L [auth C] mmCIF format, chain O [auth B]	E [auth A], I [auth D], L [auth C], O [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth D] Focus chain L [auth C] Focus chain O [auth B] Interactions & Density Focus chain E [auth A] Focus chain I [auth D] Focus chain L [auth C] Focus chain O [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.45 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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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-07-01

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: 2026-07-01
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.