8BDC | pdb_00008bdc

Human apo TRPM8 in a closed state (composite map)

PDB DOI: https://doi.org/10.2210/pdb8BDC/pdb
EM Map EMD-15981: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No
Membrane Protein: Yes PDBTM mpstruc

Deposited: 2022-10-19 Released: 2023-11-01
Deposition Author(s): Palchevskyi, S., Czarnocki-Cieciura, M., Vistoli, G., Gervasoni, S., Nowak, E., Beccari, A.R., Nowotny, M., Talarico, C.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.65 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structure of human TRPM8 channel.

Palchevskyi, S., Czarnocki-Cieciura, M., Vistoli, G., Gervasoni, S., Nowak, E., Beccari, A.R., Nowotny, M., Talarico, C.

(2023) Commun Biol 6: 1065-1065

PubMed: 37857704 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s42003-023-05425-6
Primary Citation Related Structures:
8BDC

PubMed Abstract:
TRPM8 is a non-selective cation channel permeable to both monovalent and divalent cations that is activated by multiple factors, such as temperature, voltage, pressure, and changes in osmolality. It is a therapeutic target for anticancer drug development, and its modulators can be utilized for several pathological conditions. Here, we present a cryo-electron microscopy structure of a human TRPM8 channel in the closed state that was solved at 2.7 Å resolution. Our structure comprises the most complete model of the N-terminal pre-melastatin homology region. We also visualized several lipids that are bound by the protein and modeled how the human channel interacts with icilin. Analyses of pore helices in available TRPM structures showed that all these structures can be grouped into different closed, desensitized and open state conformations based on the register of the pore helix S6 which positions particular amino acid residues at the channel constriction.

Organizational Affiliation

Laboratory of Protein Structure, International Institute of Molecular and Cell Biology in Warsaw, 02-109, Warsaw, Poland.

Macromolecule Content

Total Structure Weight: 519.36 kDa
Atom Count: 30,132
Modeled Residue Count: 3,852
Deposited Residue Count: 4,420
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transient receptor potential cation channel subfamily M member 8	A, B, C, D	1,105	Homo sapiens	Mutation(s): 0 Gene Names: TRPM8, LTRPC6, TRPP8 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q7Z2W7 (Homo sapiens) Explore Q7Z2W7 Go to UniProtKB: Q7Z2W7
PHAROS: Q7Z2W7 GTEx: ENSG00000144481
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7Z2W7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
POV Query on POV Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain L [auth B] SDF format, chain R [auth C] SDF format, chain X [auth D] MOL2 format, chain F [auth A] MOL2 format, chain L [auth B] MOL2 format, chain R [auth C] MOL2 format, chain X [auth D] mmCIF format, chain F [auth A] mmCIF format, chain L [auth B] mmCIF format, chain R [auth C] mmCIF format, chain X [auth D]	F [auth A], L [auth B], R [auth C], X [auth D]	(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate C₄₂ H₈₂ N O₈ P WTJKGGKOPKCXLL-PFDVCBLKSA-N		Interactions Focus chain F [auth A] Focus chain L [auth B] Focus chain R [auth C] Focus chain X [auth D] Interactions & Density Focus chain F [auth A] Focus chain L [auth B] Focus chain R [auth C] Focus chain X [auth D]
Y01 Query on Y01 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain M [auth B] SDF format, chain Q [auth C] SDF format, chain S [auth C] SDF format, chain W [auth D] SDF format, chain Y [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain M [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain S [auth C] MOL2 format, chain W [auth D] MOL2 format, chain Y [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain M [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain S [auth C] mmCIF format, chain W [auth D] mmCIF format, chain Y [auth D]	E [auth A] G [auth A] K [auth B] M [auth B] Q [auth C] E [auth A], G [auth A], K [auth B], M [auth B], Q [auth C], S [auth C], W [auth D], Y [auth D]	CHOLESTEROL HEMISUCCINATE C₃₁ H₅₀ O₄ WLNARFZDISHUGS-MIXBDBMTSA-N		Interactions Focus chain E [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain M [auth B] Focus chain Q [auth C] Focus chain S [auth C] Focus chain W [auth D] Focus chain Y [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain M [auth B] Focus chain Q [auth C] Focus chain S [auth C] Focus chain W [auth D] Focus chain Y [auth D]
UND Query on UND Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain N [auth B] SDF format, chain T [auth C] SDF format, chain Z [auth D] MOL2 format, chain H [auth A] MOL2 format, chain N [auth B] MOL2 format, chain T [auth C] MOL2 format, chain Z [auth D] mmCIF format, chain H [auth A] mmCIF format, chain N [auth B] mmCIF format, chain T [auth C] mmCIF format, chain Z [auth D]	H [auth A], N [auth B], T [auth C], Z [auth D]	UNDECANE C₁₁ H₂₄ RSJKGSCJYJTIGS-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain N [auth B] Focus chain T [auth C] Focus chain Z [auth D] Interactions & Density Focus chain H [auth A] Focus chain N [auth B] Focus chain T [auth C] Focus chain Z [auth D]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain BA [auth D] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain U [auth C] SDF format, chain V [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] mmCIF format, chain AA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C]	AA [auth D] BA [auth D] I [auth A] J [auth A] O [auth B] AA [auth D], BA [auth D], I [auth A], J [auth A], O [auth B], P [auth B], U [auth C], V [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain U [auth C] Focus chain V [auth C] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain U [auth C] Focus chain V [auth C]