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- EMDB-40600: Focused map of the cytoplasmic domains of rat TRPM5, conformation... -

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Basic information

Entry
Database: EMDB / ID: EMD-40600
TitleFocused map of the cytoplasmic domains of rat TRPM5, conformation trace-1
Map dataFocused map of the cytoplasmic domains of rat TRPM5, conformation trace-1, sharpened
Sample
  • Complex: Transient Receptor Potential Melastatin 5 (TRPM5)
Keywordsion channel / Transient Receptor Potential / TRP / Transient Receptor Potential Melastatin 5 / TRPM5 / MEMBRANE PROTEIN
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsKaruppan S / Schrag LG / Jara-Oseguera A / Zubcevic L
Funding support United States, 2 items
OrganizationGrant numberCountry
Other private United States
Other privaten/a, Start-up funds
CitationJournal: Proc Natl Acad Sci U S A / Year: 2024
Title: Structural dynamics at cytosolic interprotomer interfaces control gating of a mammalian TRPM5 channel.
Authors: Sebastian Karuppan / Lynn Goss Schrag / Caroline M Pastrano / Andrés Jara-Oseguera / Lejla Zubcevic /
Abstract: The transient receptor potential melastatin (TRPM) tetrameric cation channels are involved in a wide range of biological functions, from temperature sensing and taste transduction to regulation of ...The transient receptor potential melastatin (TRPM) tetrameric cation channels are involved in a wide range of biological functions, from temperature sensing and taste transduction to regulation of cardiac function, inflammatory pain, and insulin secretion. The structurally conserved TRPM cytoplasmic domains make up >70 % of the total protein. To investigate the mechanism by which the TRPM cytoplasmic domains contribute to gating, we employed electrophysiology and cryo-EM to study TRPM5-a channel that primarily relies on activation via intracellular Ca. Here, we show that activation of mammalian TRPM5 channels is strongly altered by Ca-dependent desensitization. Structures of rat TRPM5 identify a series of conformational transitions triggered by Ca binding, whereby formation and dissolution of cytoplasmic interprotomer interfaces appear to control activation and desensitization of the channel. This study shows the importance of the cytoplasmic assembly in TRPM5 channel function and sets the stage for future investigations of other members of the TRPM family.
History
DepositionApr 26, 2023-
Header (metadata) releaseJul 3, 2024-
Map releaseJul 3, 2024-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40600.png

Downloads & links

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Map

FileDownload / File: emd_40600.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFocused map of the cytoplasmic domains of rat TRPM5, conformation trace-1, sharpened
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 360 pix.
= 388.8 Å		1.08 Å/pix.
x 360 pix.
= 388.8 Å		1.08 Å/pix.
x 360 pix.
= 388.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.17
Minimum - Maximum-1.1322476 - 2.241336
Average (Standard dev.)0.0027789045 (±0.022000816)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 388.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Focused map of the cytoplasmic domains of rat...

Fileemd_40600_additional_1.map
AnnotationFocused map of the cytoplasmic domains of rat TRPM5, conformation trace-1, not sharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Focused map of the cytoplasmic domains of rat...

Fileemd_40600_half_map_1.map
AnnotationFocused map of the cytoplasmic domains of rat TRPM5, conformation trace-1, half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Focused map of the cytoplasmic domains of rat...

Fileemd_40600_half_map_2.map
AnnotationFocused map of the cytoplasmic domains of rat TRPM5, conformation trace-1, half map B
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 Melastatin 5 (TRPM5)

EntireName: Transient Receptor Potential Melastatin 5 (TRPM5)
Components
  • Complex: Transient Receptor Potential Melastatin 5 (TRPM5)

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Supramolecule #1: Transient Receptor Potential Melastatin 5 (TRPM5)

SupramoleculeName: Transient Receptor Potential Melastatin 5 (TRPM5) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 520 KDa

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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

Concentration3 mg/mL
BufferpH: 8
GridModel: UltrAuFoil R1.2/1.3 / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 296.15 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2601822
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.2) / Number images used: 52230
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

Initial modelPDB ID:

8sl6


Chain - Source name: Other / Chain - Initial model type: other / Details: model generated in this study
RefinementProtocol: RIGID BODY FIT

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