8E4L | pdb_00008e4l

The open state mouse TRPM8 structure in complex with the cooling agonist C3, AITC, and PI(4,5)P2

PDB DOI: https://doi.org/10.2210/pdb8E4L/pdb
EM Map EMD-27891: EMDB EMDataResource

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

Deposited: 2022-08-18 Released: 2022-10-26
Deposition Author(s): Yin, Y., Zhang, F., Feng, S., Butay, K.J., Borgnia, M.J., 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: 3.32 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Activation mechanism of the mouse cold-sensing TRPM8 channel by cooling agonist and PIP 2.

Yin, Y., Zhang, F., Feng, S., Butay, K.J., Borgnia, M.J., Im, W., Lee, S.Y.

(2022) Science 378: eadd1268-eadd1268

PubMed: 36227998 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/science.add1268
Primary Citation Related Structures:
8E4L, 8E4M, 8E4N, 8E4O, 8E4P, 8E4Q

PubMed Abstract:
The transient receptor potential melastatin 8 (TRPM8) channel is the primary molecular transducer responsible for the cool sensation elicited by menthol and cold in mammals. TRPM8 activation is controlled by cooling compounds together with the membrane lipid phosphatidylinositol 4,5-bisphosphate (PIP ₂). Our knowledge of cold sensation and the therapeutic potential of TRPM8 for neuroinflammatory diseases and pain will be enhanced by understanding the structural basis of cooling agonist- and PIP ₂-dependent TRPM8 activation. We present cryo-electron microscopy structures of mouse TRPM8 in closed, intermediate, and open states along the ligand- and PIP ₂-dependent gating pathway. Our results uncover two discrete agonist sites, state-dependent rearrangements in the gate positions, and a disordered-to-ordered transition of the gate-forming S6-elucidating the molecular basis of chemically induced cool sensation in mammals.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 530.78 kDa
Atom Count: 27,976
Modeled Residue Count: 3,592
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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PIO Query on PIO Download:Ideal Coordinates CCD File SDF format, chain T [auth D] SDF format, chain P [auth C] SDF format, chain L [auth B] SDF format, chain H [auth A] MOL2 format, chain T [auth D] MOL2 format, chain P [auth C] MOL2 format, chain L [auth B] MOL2 format, chain H [auth A] mmCIF format, chain T [auth D] mmCIF format, chain P [auth C] mmCIF format, chain L [auth B] mmCIF format, chain H [auth A]	H [auth A], L [auth B], P [auth C], T [auth D]	[(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate C₂₅ H₄₉ O₁₉ P₃ XLNCEHRXXWQMPK-MJUMVPIBSA-N		Interactions Focus chain H [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain T [auth D] Interactions & Density Focus chain H [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain T [auth D]
ULO Query on ULO Download:Ideal Coordinates CCD File SDF format, chain S [auth D] SDF format, chain O [auth C] SDF format, chain K [auth B] SDF format, chain G [auth A] MOL2 format, chain S [auth D] MOL2 format, chain O [auth C] MOL2 format, chain K [auth B] MOL2 format, chain G [auth A] mmCIF format, chain S [auth D] mmCIF format, chain O [auth C] mmCIF format, chain K [auth B] mmCIF format, chain G [auth A]	G [auth A], K [auth B], O [auth C], S [auth D]	nonyl(oxo)di(propan-2-yl)-lambda~5~-phosphane C₁₅ H₃₃ O P DHOTYMJGZIUWRT-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain S [auth D] Interactions & Density Focus chain G [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain S [auth D]
UL9 Query on UL9 Download:Ideal Coordinates CCD File SDF format, chain R [auth D] SDF format, chain N [auth C] SDF format, chain J [auth B] SDF format, chain F [auth A] MOL2 format, chain R [auth D] MOL2 format, chain N [auth C] MOL2 format, chain J [auth B] MOL2 format, chain F [auth A] mmCIF format, chain R [auth D] mmCIF format, chain N [auth C] mmCIF format, chain J [auth B] mmCIF format, chain F [auth A]	F [auth A], J [auth B], N [auth C], R [auth D]	3-isothiocyanatoprop-1-ene C₄ H₅ N S ZOJBYZNEUISWFT-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain R [auth D] Interactions & Density Focus chain F [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain R [auth D]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain Q [auth D] SDF format, chain M [auth C] SDF format, chain I [auth B] SDF format, chain E [auth A] MOL2 format, chain Q [auth D] MOL2 format, chain M [auth C] MOL2 format, chain I [auth B] MOL2 format, chain E [auth A] mmCIF format, chain Q [auth D] mmCIF format, chain M [auth C] mmCIF format, chain I [auth B] mmCIF format, chain E [auth A]	E [auth A], I [auth B], M [auth C], Q [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain Q [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain Q [auth D]

Binding Affinity Annotations
ID	Source	Binding Affinity
ULO	BindingDB: 8E4L	EC50: 900 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.32 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	PHENIX

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-10-26

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Eye Institute (NIH/NEI)	United States	R01EY031698
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	R35NS097241