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- EMDB-71352: Avian TRPM8 (Parus major) closed, ligand-free structure resolved ... -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-71352
TitleAvian TRPM8 (Parus major) closed, ligand-free structure resolved in cell vesicles using cryo-EM
Map data
Sample
  • Complex: Homotetrameric complex of Parus major TRPM8 determined in a cell-derived vesicles.
    • Protein or peptide: Transient receptor potential cation channel subfamily M member 8
KeywordsTRPM8 / transient receptor potential melastatin 8 / MEMBRANE PROTEIN / Parus major
Function / homology
Function and homology information


ligand-gated calcium channel activity / plasma membrane
Similarity search - Function
: / TRPM, SLOG domain / : / SLOG in TRPM / TRPM2-like domain / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Transient receptor potential cation channel subfamily M member 8
Similarity search - Component
Biological speciesParus major (Great Tit)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsChoi KY / Lin X / Cheng Y / Julius D
Funding support United States, 3 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R35NS105038 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM140847 United States
CitationJournal: Nature / Year: 2026
Title: Structural energetics of cold sensitivity
Authors: Choi KY / Lin X / Cheng Y / Julius D
History
DepositionJun 21, 2025-
Header (metadata) releaseMar 25, 2026-
Map releaseMar 25, 2026-
UpdateMar 25, 2026-
Current statusMar 25, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71352.png

Downloads & links

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Map

FileDownload / File: emd_71352.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 320 pix.
= 262.048 Å		0.82 Å/pix.
x 320 pix.
= 262.048 Å		0.82 Å/pix.
x 320 pix.
= 262.048 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8189 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.012
Minimum - Maximum-0.08422595 - 0.12745042
Average (Standard dev.)0.00020296291 (±0.004564294)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 262.048 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_71352_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_71352_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_71352_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Homotetrameric complex of Parus major TRPM8 determined in a cell-...

EntireName: Homotetrameric complex of Parus major TRPM8 determined in a cell-derived vesicles.
Components
  • Complex: Homotetrameric complex of Parus major TRPM8 determined in a cell-derived vesicles.
    • Protein or peptide: Transient receptor potential cation channel subfamily M member 8

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Supramolecule #1: Homotetrameric complex of Parus major TRPM8 determined in a cell-...

SupramoleculeName: Homotetrameric complex of Parus major TRPM8 determined in a cell-derived vesicles.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Parus major (Great Tit)

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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: Parus major (Great Tit)
Molecular weightTheoretical: 127.217016 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GPGSGSGMRH RRNGNFESSR LLYSSMSRSI DVACSDADLA NFIQENFKKR ECVFFTKDTK SMGNLCKCGY PENQHIEGTQ VNTTEKWNY KKHTKELPTD AFGDIQFENL GKRGKYIRLS CDTDSETLYD LMTQHWHLKT PNLVISVTGG AKNFALKPRM R KIFSRLIY ...String:
GPGSGSGMRH RRNGNFESSR LLYSSMSRSI DVACSDADLA NFIQENFKKR ECVFFTKDTK SMGNLCKCGY PENQHIEGTQ VNTTEKWNY KKHTKELPTD AFGDIQFENL GKRGKYIRLS CDTDSETLYD LMTQHWHLKT PNLVISVTGG AKNFALKPRM R KIFSRLIY IAQSKGAWIF TGGTHYGLMK YIGEVVRDNT ISRSSEENVV AIGIAAWGMI SNRETLIRTA DSDGSFLARY IM DDLKRDP LYCLDNNHTH LLLVDNGTHG HPTTEAKVRT QLEKYISERV IPESNYGGKI PIVCFAQGGG KETLKSINVA IKS KIPCVV VEGSGRIADV IASLVEAEGT LASSCVKESL LRFLPRTISR LSEEETESWI KWIKEVLESP HLLTVIKIEE AGDE IVSNA ISFALYKAFS TNEHDRDNWN GQLKLLLEWN QLDLASDEIF TNDRNWESAD LQDVMFTALV KDRPKFVRLF LENGL NLRK FLTTEVLREL YTNNFSSLVF KNLQIAKNSY NDALLTFVWK MVEDFRRGFK RDYKNSKDEM EIQLSEECPI TRHPLQ ALF IWSVLQNKKE LSKVIWEQTR GCTLAALGAS KLLKSMAKVK NDINAAGESE ELANEYETRA VELFTECYSN DEDLAEQ LL TYSCEAWGGS NCLELAVEAR DQQFIAQPGV QNFLSKQWYG EISRDTKNWK IIMCLFFFPL IGCGFISFRK KPVEKSKK L FLYYVSFFTS PFVVFSWNVI FYIAFLLLFA YVLLMDFQKE PTALEIILYV LVFVLLCDEV RQWYMNGSKY FSDLWNVMD TLAIFYFIAG IVFRLHSDES SWYSGRVIFC LDYIVFTLRL IHIFTVSRNL GPKIIMLQRM MIDVFFFLFL FAVWMVAFGV ARQGILRKN EHRWEWIFRS VIYEPYLAMF GQYPDDIDGT TYNFDRCTFS GNESKPLCVE LDANNQPRFP EWITIPLVCI Y MLSTNILL VNLLVAMFGY TVGSVQENND QVWKFQRFFL VQEYCSRLTI PFPFVIFAYI FMVMRKCFKC CCNKESKEPS IC CSRNEDN EILAWEAVMK ENYLVKINTK ANDSSEEMVH RFRQLDAKLS DLKGLLKEIS SKIK

UniProtKB: Transient receptor potential cation channel subfamily M member 8

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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: 7.4
Component:
ConcentrationFormulaName
300.0 mMKClpotassium chloride
20.0 mMC8H18N2O4SHEPES
0.5 mMC13H17F13NO4PFos-Choline-8, Fluorinated
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 4 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 35382 / Average exposure time: 2.0 sec. / Average electron dose: 47.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Details: Initial model determined from a screening dataset and used as an initial reference.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5) / Number images used: 134664
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5)

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