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- EMDB-32725: Mouse TRPM8 in lipid nanodiscs in the presence of calcium, icilin... -

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Basic information

Entry
Database: EMDB / ID: EMD-32725
TitleMouse TRPM8 in lipid nanodiscs in the presence of calcium, icilin and PI(4,5)P2
Map datananodisc-ca-icilin-pip2
Sample
  • Complex: Mouse TRPM8 in lipid nanodiscs in the presence of calcium, icilin and PI(4,5)P2
    • Protein or peptide: Transient receptor potential cation channel subfamily M member 8
  • Ligand: CALCIUM ION
  • Ligand: SODIUM ION
  • Ligand: Icilin
KeywordsTRPM8 / TRANSPORT PROTEIN
Function / homology
Function and homology information


ligand-gated calcium channel activity / TRP channels / thermoception / response to temperature stimulus / monoatomic ion channel activity / response to cold / calcium ion transmembrane transport / calcium channel activity / intracellular calcium ion homeostasis / calcium ion transport ...ligand-gated calcium channel activity / TRP channels / thermoception / response to temperature stimulus / monoatomic ion channel activity / response to cold / calcium ion transmembrane transport / calcium channel activity / intracellular calcium ion homeostasis / calcium ion transport / positive regulation of cold-induced thermogenesis / membrane raft / external side of plasma membrane / identical protein binding / membrane / 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: 3.04 Å
AuthorsZhao C / Xie Y
Funding support China, 2 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2020YFA0908501 China
Ministry of Science and Technology (MoST, China)2018YFA0508100 China
CitationJournal: Nat Commun / Year: 2022
Title: Structures of a mammalian TRPM8 in closed state.
Authors: Cheng Zhao / Yuan Xie / Lizhen Xu / Fan Ye / Ximing Xu / Wei Yang / Fan Yang / Jiangtao Guo /
Abstract: Transient receptor potential melastatin 8 (TRPM8) channel is a Ca-permeable non-selective cation channel that acts as the primary cold sensor in humans. TRPM8 is also activated by ligands such as ...Transient receptor potential melastatin 8 (TRPM8) channel is a Ca-permeable non-selective cation channel that acts as the primary cold sensor in humans. TRPM8 is also activated by ligands such as menthol, icilin, and phosphatidylinositol 4,5-bisphosphate (PIP), and desensitized by Ca. Here we have determined electron cryo-microscopy structures of mouse TRPM8 in the absence of ligand, and in the presence of Ca and icilin at 2.5-3.2 Å resolution. The ligand-free state TRPM8 structure represents the full-length structure of mammalian TRPM8 channels with a canonical S4-S5 linker and the clearly resolved selectivity filter and outer pore loop. TRPM8 has a short but wide selectivity filter which may account for its permeability to hydrated Ca. Ca and icilin bind in the cytosolic-facing cavity of the voltage-sensing-like domain of TRPM8 but induce little conformational change. All the ligand-bound TRPM8 structures adopt the same closed conformation as the ligand-free structure. This study reveals the overall architecture of mouse TRPM8 and the structural basis for its ligand recognition.
History
DepositionJan 26, 2022-
Header (metadata) releaseJun 22, 2022-
Map releaseJun 22, 2022-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32725.png

Downloads & links

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Map

FileDownload / File: emd_32725.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationnanodisc-ca-icilin-pip2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 250 pix.
= 253.5 Å		1.01 Å/pix.
x 250 pix.
= 253.5 Å		1.01 Å/pix.
x 250 pix.
= 253.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.014 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.013
Minimum - Maximum-0.045785587 - 0.087922275
Average (Standard dev.)-0.0000086242535 (±0.003496276)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions250250250
Spacing250250250
CellA=B=C: 253.50002 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Mouse TRPM8 in lipid nanodiscs in the presence of calcium, icilin...

EntireName: Mouse TRPM8 in lipid nanodiscs in the presence of calcium, icilin and PI(4,5)P2
Components
  • Complex: Mouse TRPM8 in lipid nanodiscs in the presence of calcium, icilin and PI(4,5)P2
    • Protein or peptide: Transient receptor potential cation channel subfamily M member 8
  • Ligand: CALCIUM ION
  • Ligand: SODIUM ION
  • Ligand: Icilin

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Supramolecule #1: Mouse TRPM8 in lipid nanodiscs in the presence of calcium, icilin...

SupramoleculeName: Mouse TRPM8 in lipid nanodiscs in the presence of calcium, icilin and PI(4,5)P2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)

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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: 129.542227 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSFEGARLSM RSRRNGTMGS TRTLYSSVSR STDVSYSDSD LVNFIQANFK KRECVFFTRD SKAMENICKC GYAQSQHIEG TQINQNEKW NYKKHTKEFP TDAFGDIQFE TLGKKGKYLR LSCDTDSETL YELLTQHWHL KTPNLVISVT GGAKNFALKP R MRKIFSRL ...String:
MSFEGARLSM RSRRNGTMGS TRTLYSSVSR STDVSYSDSD LVNFIQANFK KRECVFFTRD SKAMENICKC GYAQSQHIEG TQINQNEKW NYKKHTKEFP TDAFGDIQFE TLGKKGKYLR LSCDTDSETL YELLTQHWHL KTPNLVISVT GGAKNFALKP R MRKIFSRL IYIAQSKGAW ILTGGTHYGL MKYIGEVVRD NTISRNSEEN IVAIGIAAWG MVSNRDTLIR SCDDEGHFSA QY IMDDFTR DPLYILDNNH THLLLVDNGC HGHPTVEAKL RNQLEKYISE RTSQDSNYGG KIPIVCFAQG GGRETLKAIN TSV KSKIPC VVVEGSGQIA DVIASLVEVE DVLTSSMVKE KLVRFLPRTV SRLPEEEIES WIKWLKEILE SSHLLTVIKM EEAG DEIVS NAISYALYKA FSTNEQDKDN WNGQLKLLLE WNQLDLASDE IFTNDRRWES ADLQEVMFTA LIKDRPKFVR LFLEN GLNL QKFLTNEVLT ELFSTHFSTL VYRNLQIAKN SYNDALLTFV WKLVANFRRS FWKEDRSSRE DLDVELHDAS LTTRHP LQA LFIWAILQNK KELSKVIWEQ TKGCTLAALG ASKLLKTLAK VKNDINAAGE SEELANEYET RAVELFTECY SNDEDLA EQ LLVYSCEAWG GSNCLELAVE ATDQHFIAQP GVQNFLSKQW YGEISRDTKN WKIILCLFII PLVGCGLVSF RKKPIDKH K KLLWYYVAFF TSPFVVFSWN VVFYIAFLLL FAYVLLMDFH SVPHTPELIL YALVFVLFCD EVRQWYMNGV NYFTDLWNV MDTLGLFYFI AGIVFRLHSS NKSSLYSGRV IFCLDYIIFT LRLIHIFTVS RNLGPKIIML QRMLIDVFFF LFLFAVWMVA FGVARQGIL RQNEQRWRWI FRSVIYEPYL AMFGQVPSDV DSTTYDFSHC TFSGNESKPL CVELDEHNLP RFPEWITIPL V CIYMLSTN ILLVNLLVAM FGYTVGIVQE NNDQVWKFQR YFLVQEYCNR LNIPFPFVVF AYFYMVVKKC FKCCCKEKNM ES NACCFRN EDNETLAWEG VMKENYLVKI NTKANDNSEE MRHRFRQLDS KLNDLKSLLK EIANNIKLEG GSSGGWSHPQ FEK

UniProtKB: Transient receptor potential cation channel subfamily M member 8

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Macromolecule #2: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 4 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #3: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 3 / Number of copies: 1
Molecular weightTheoretical: 22.99 Da

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Macromolecule #4: Icilin

MacromoleculeName: Icilin / type: ligand / ID: 4 / Number of copies: 4 / Formula: KX7
Molecular weightTheoretical: 311.292 Da
Chemical component information

ChemComp-KX7:
Icilin / agonist*YM

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 62.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Nominal defocus max: 1.3 µm / Nominal defocus min: 1.1 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 62791
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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