9B6G | pdb_00009b6g

Cryo-EM structure of the mouse TRPM8 channel in complex with the antagonist AMTB

PDB DOI: https://doi.org/10.2210/pdb9B6G/pdb
EM Map EMD-44258: EMDB EMDataResource

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

Deposited: 2024-03-25 Released: 2024-08-21
Deposition Author(s): Yin, Y., Park, C.-G., Zhang, F., Fedor, J., Feng, S., Suo, Y., Im, W., Lee, S.-Y.
Funding Organization(s): National Institutes of Health/National Eye Institute (NIH/NEI), National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.81 Å
Resolution: 2.81 Å
Resolution: 2.81 Å
Resolution: 2.81 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Mechanisms of sensory adaptation and inhibition of the cold and menthol receptor TRPM8.

Yin, Y., Park, C.G., Zhang, F., G Fedor, J., Feng, S., Suo, Y., Im, W., Lee, S.Y.

(2024) Sci Adv 10: eadp2211-eadp2211

PubMed: 39093967 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/sciadv.adp2211
Primary Citation Related Structures:
9B6D, 9B6E, 9B6F, 9B6G, 9B6H, 9B6I, 9B6J, 9B6K

PubMed Abstract:
Our sensory adaptation to cold and chemically induced coolness is mediated by the intrinsic property of TRPM8 channels to desensitize. TRPM8 is also implicated in cold-evoked pain disorders and migraine, highlighting its inhibitors as an avenue for pain relief. Despite the importance, the mechanisms of TRPM8 desensitization and inhibition remained unclear. We found, using cryo-electron microscopy, electrophysiology, and molecular dynamics simulations, that TRPM8 inhibitors bind selectively to the desensitized state of the channel. These inhibitors were used to reveal the overlapping mechanisms of desensitization and inhibition and that cold and cooling agonists share a common desensitization pathway. Furthermore, we identified the structural determinants crucial for the conformational change in TRPM8 desensitization. Our study illustrates how receptor-level conformational changes alter cold sensation, providing insights into therapeutic development.

Organizational Affiliation

Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA.

Macromolecule Content

Total Structure Weight: 538.39 kDa
Atom Count: 28,484
Modeled Residue Count: 3,660
Deposited Residue Count: 4,540
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	1,135	Mus musculus	Mutation(s): 0 Gene Names: Trpm8, Ltrpc6, Trpp8 Membrane Entity: Yes
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
Y01 Query on Y01 Download:Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain DA [auth D] SDF format, chain E [auth A] SDF format, chain EA [auth D] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain Q [auth B] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain Z [auth D] SDF format, chain U [auth C] SDF format, chain P [auth B] SDF format, chain N [auth B] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain Z [auth D] MOL2 format, chain U [auth C] MOL2 format, chain P [auth B] MOL2 format, chain N [auth B] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain AA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain E [auth A] mmCIF format, chain EA [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C] mmCIF format, chain Z [auth D] mmCIF format, chain U [auth C] mmCIF format, chain P [auth B] mmCIF format, chain N [auth B] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain AA [auth D]	AA [auth D] BA [auth D] DA [auth D] E [auth A] EA [auth D] AA [auth D], BA [auth D], DA [auth D], E [auth A], EA [auth D], F [auth A], G [auth A], I [auth A], J [auth A], L [auth B], M [auth B], N [auth B], P [auth B], Q [auth B], S [auth C], T [auth C], U [auth C], W [auth C], X [auth C], Z [auth D]	CHOLESTEROL HEMISUCCINATE C₃₁ H₅₀ O₄ WLNARFZDISHUGS-MIXBDBMTSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain DA [auth D] Focus chain E [auth A] Focus chain EA [auth D] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain DA [auth D] Focus chain E [auth A] Focus chain EA [auth D] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Z [auth D]
LQ7 (Subject of Investigation/LOI) Query on LQ7 Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain O [auth B] SDF format, chain V [auth C] SDF format, chain CA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain O [auth B] MOL2 format, chain V [auth C] MOL2 format, chain CA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain O [auth B] mmCIF format, chain V [auth C] mmCIF format, chain CA [auth D]	CA [auth D], H [auth A], O [auth B], V [auth C]	N-(3-aminopropyl)-2-[(3-methylphenyl)methoxy]-N-[(thiophen-2-yl)methyl]benzamide C₂₃ H₂₆ N₂ O₂ S LCQJRANJHOEQFG-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain H [auth A] Focus chain O [auth B] Focus chain V [auth C] Interactions & Density Focus chain CA [auth D] Focus chain H [auth A] Focus chain O [auth B] Focus chain V [auth C]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain FA [auth D] SDF format, chain K [auth A] SDF format, chain R [auth B] SDF format, chain Y [auth C] MOL2 format, chain FA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain R [auth B] MOL2 format, chain Y [auth C] mmCIF format, chain FA [auth D] mmCIF format, chain K [auth A] mmCIF format, chain R [auth B] mmCIF format, chain Y [auth C]	FA [auth D], K [auth A], R [auth B], Y [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain FA [auth D] Focus chain K [auth A] Focus chain R [auth B] Focus chain Y [auth C] Interactions & Density Focus chain FA [auth D] Focus chain K [auth A] Focus chain R [auth B] Focus chain Y [auth C]

Binding Affinity Annotations
ID	Source	Binding Affinity
LQ7	BindingDB: 9B6G	IC50: min: 4, max: 7300 (nM) from 10 assay(s)

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.81 Å
Resolution: 2.81 Å
Resolution: 2.81 Å
Resolution: 2.81 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-08-21

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Eye Institute (NIH/NEI)	United States	--
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	--