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- EMDB-27893: The closed C1-state mouse TRPM8 structure in complex with PI(4,5)P2 -

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Basic information

Entry
Database: EMDB / ID: EMD-27893
TitleThe closed C1-state mouse TRPM8 structure in complex with PI(4,5)P2
Map dataFull map, sharpened with B-factor -10
Sample
  • Complex: Transient receptor potential cation channel subfamily M member 8
    • Protein or peptide: Transient receptor potential cation channel subfamily M member 8
  • Ligand: [(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
Function / homology
Function and homology information


ligand-gated calcium channel activity / TRP channels / thermoception / response to temperature stimulus / response to cold / calcium ion transmembrane transport / calcium channel activity / intracellular calcium ion homeostasis / calcium ion transport / monoatomic ion channel activity ...ligand-gated calcium channel activity / TRP channels / thermoception / response to temperature stimulus / response to cold / calcium ion transmembrane transport / calcium channel activity / intracellular calcium ion homeostasis / calcium ion transport / monoatomic ion channel activity / positive regulation of cold-induced thermogenesis / membrane raft / external side of plasma membrane / membrane / identical protein binding / plasma membrane
Similarity search - Function
TRPM, SLOG domain / SLOG in TRPM / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Transient receptor potential cation channel subfamily M member 8
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.07 Å
AuthorsYin Y / Zhang F / Feng S / Butay KJ / Borgnia MJ / Im W / Lee S-Y
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI)R01EY031698 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R35NS097241 United States
CitationJournal: Science / Year: 2022
Title: Activation mechanism of the mouse cold-sensing TRPM8 channel by cooling agonist and PIP.
Authors: Ying Yin / Feng Zhang / Shasha Feng / Kevin John Butay / Mario J Borgnia / Wonpil Im / Seok-Yong Lee /
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 ...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). 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-dependent TRPM8 activation. We present cryo-electron microscopy structures of mouse TRPM8 in closed, intermediate, and open states along the ligand- and PIP-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.
History
DepositionAug 18, 2022-
Header (metadata) releaseOct 26, 2022-
Map releaseOct 26, 2022-
UpdateOct 26, 2022-
Current statusOct 26, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27893.png

Downloads & links

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Map

FileDownload / File: emd_27893.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFull map, sharpened with B-factor -10
Voxel sizeX=Y=Z: 1.056 Å
Density
Contour LevelBy AUTHOR: 0.14
Minimum - Maximum-0.55751663 - 1.295709
Average (Standard dev.)0.0026034797 (±0.040135108)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 337.91998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_27893_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_27893_half_map_1.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_27893_half_map_2.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Transient receptor potential cation channel subfamily M member 8

EntireName: Transient receptor potential cation channel subfamily M member 8
Components
  • Complex: Transient receptor potential cation channel subfamily M member 8
    • Protein or peptide: Transient receptor potential cation channel subfamily M member 8
  • Ligand: [(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

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Supramolecule #1: Transient receptor potential cation channel subfamily M member 8

SupramoleculeName: Transient receptor potential cation channel subfamily M member 8
type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Homo sapiens (human)

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Macromolecule #1: Transient receptor potential cation channel subfamily M member 8

MacromoleculeName: Transient receptor potential cation channel subfamily M member 8
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 131.548312 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MASFEGARLS MRSRRNGTMG STRTLYSSVS RSTDVSYSDS DLVNFIQANF KKRECVFFTR DSKAMENICK CGYAQSQHIE GTQINQNEK WNYKKHTKEF PTDAFGDIQF ETLGKKGKYL RLSCDTDSET LYELLTQHWH LKTPNLVISV TGGAKNFALK P RMRKIFSR ...String:
MASFEGARLS MRSRRNGTMG STRTLYSSVS RSTDVSYSDS DLVNFIQANF KKRECVFFTR DSKAMENICK CGYAQSQHIE GTQINQNEK WNYKKHTKEF PTDAFGDIQF ETLGKKGKYL RLSCDTDSET LYELLTQHWH LKTPNLVISV TGGAKNFALK P RMRKIFSR LIYIAQSKGA WILTGGTHYG LMKYIGEVVR DNTISRNSEE NIVAIGIAAW GMVSNRDTLI RSCDDEGHFS AQ YIMDDFT RDPLYILDNN HTHLLLVDNG CHGHPTVEAK LRNQLEKYIS ERTSQDSNYG GKIPIVCFAQ GGGRETLKAI NTS VKSKIP CVVVEGSGQI ADVIASLVEV EDVLTSSMVK EKLVRFLPRT VSRLPEEEIE SWIKWLKEIL ESSHLLTVIK MEEA GDEIV SNAISYALYK AFSTNEQDKD NWNGQLKLLL EWNQLDLASD EIFTNDRRWE SADLQEVMFT ALIKDRPKFV RLFLE NGLN LQKFLTNEVL TELFSTHFST LVYRNLQIAK NSYNDALLTF VWKLVANFRR SFWKEDRSSR EDLDVELHDA SLTTRH PLQ ALFIWAILQN KKELSKVIWE QTKGCTLAAL GASKLLKTLA KVKNDINAAG ESEELANEYE TRAVELFTEC YSNDEDL AE QLLVYSCEAW GGSNCLELAV EATDQHFIAQ PGVQNFLSKQ WYGEISRDTK NWKIILCLFI IPLVGCGLVS FRKKPIDK H KKLLWYYVAF FTSPFVVFSW NVVFYIAFLL LFAYVLLMDF HSVPHTPELI LYALVFVLFC DEVRQWYMNG VNYFTDLWN VMDTLGLFYF IAGIVFRLHS SNKSSLYSGR VIFCLDYIIF TLRLIHIFTV SRNLGPKIIM LQRMLIDVFF FLFLFAVWMV AFGVARQGI LRQNEQRWRW IFRSVIYEPY LAMFGQVPSD VDSTTYDFSH CTFSGNESKP LCVELDEHNL PRFPEWITIP L VCIYMLST NILLVNLLVA MFGYTVGIVQ ENNDQVWKFQ RYFLVQEYCN RLNIPFPFVV FAYFYMVVKK CFKCCCKEKN ME SNACCFR NEDNETLAWE GVMKENYLVK INTKANDNSE EMRHRFRQLD SKLNDLKSLL KEIANNIKSN SLEVLFQGPD YKD DDDKAH HHHHHHHHH

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Macromolecule #2: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(o...

MacromoleculeName: [(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
type: ligand / ID: 2 / Number of copies: 4 / Formula: PIO
Molecular weightTheoretical: 746.566 Da
Chemical component information

ChemComp-PIO:
[(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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2.0 nm / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 81000
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 12071 / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3628779
CTF correctionSoftware: (Name: Gctf, RELION)
Startup modelType of model: EMDB MAP
EMDB ID:

7127


Details: The EM map for the previously reported apo TRPM8 structure (EMD-7127) was low-pass filtered to 30-Angstrom and used as an initial model without a reference mask.
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 83727
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8e4n:
The closed C1-state mouse TRPM8 structure in complex with PI(4,5)P2

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