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- EMDB-40575: Cryo-EM structure of the rat TRPM5 channel in trace calcium, trace-1 -

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Basic information

Entry
Database: EMDB / ID: EMD-40575
TitleCryo-EM structure of the rat TRPM5 channel in trace calcium, trace-1
Map data
Sample
  • Complex: Transient Receptor Potential Melastatin 5 (TRPM5)
    • Protein or peptide: Transient receptor potential cation channel subfamily M member 5
Keywordsion channel / Transient Receptor Potential / TRP / Transient Receptor Potential Melastatin 5 / TRPM5 / MEMBRANE PROTEIN
Function / homology
Function and homology information


ligand-gated calcium channel activity / calcium-activated cation channel activity / sodium channel activity / potassium channel activity / potassium ion transmembrane transport / calcium ion transmembrane transport / monoatomic ion transmembrane transport / neuronal cell body / dendrite / 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 5
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 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 21, 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_40575.png

Downloads & links

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Map

FileDownload / File: emd_40575.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
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)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.11
Minimum - Maximum-0.3384559 - 0.7012971
Average (Standard dev.)0.0027173478 (±0.02207593)
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 for cytosolic domains, sharp

Fileemd_40575_additional_1.map
AnnotationFocused map for cytosolic domains, sharp
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: Focused map for cytosolic domains, not sharpened

Fileemd_40575_additional_2.map
AnnotationFocused map for cytosolic domains, not sharpened
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Additional map: Focused map for cytosolic domains, half map A

Fileemd_40575_additional_3.map
AnnotationFocused map for cytosolic domains, half map A
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: Focused map for cytosolic domains, half map B

Fileemd_40575_additional_4.map
AnnotationFocused map for cytosolic domains, half map B
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_40575_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_40575_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

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Slices (1/2)
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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)
    • Protein or peptide: Transient receptor potential cation channel subfamily M member 5

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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: all
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 520 KDa

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Macromolecule #1: Transient receptor potential cation channel subfamily M member 5

MacromoleculeName: Transient receptor potential cation channel subfamily M member 5
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 132.351719 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYKDDDDKL EMPMAQSSCP GSPPDTGDGW EPVLCKGEVN FGGSGKKRSK FVKVPSNVAP SMLFELLLTE WHLPAPNLVV SLVGEERLF AMKSWLRDVL RKGLVKAAQS TGAWILTSAL HVGLARHVGQ AVRDHSLAST STKVRVVAIG MASLDRILHR Q LLDGVQAQ ...String:
MDYKDDDDKL EMPMAQSSCP GSPPDTGDGW EPVLCKGEVN FGGSGKKRSK FVKVPSNVAP SMLFELLLTE WHLPAPNLVV SLVGEERLF AMKSWLRDVL RKGLVKAAQS TGAWILTSAL HVGLARHVGQ AVRDHSLAST STKVRVVAIG MASLDRILHR Q LLDGVQAQ EDTPIHYPAD EGSTQGPLCP LDSNLSHFIL VEPGTLGSGN DGLAELQLSL EKHISQQRTG YGGTSSIQIP VL CLLVNGD PSTLERMSRA VEQAAPWLIL AGSGGIADVL AALVGQPHLL VPQVTEKQFR EKFPSECFSW EAIVHWTELL QNI AAHPHL LTVYDFEQEG SEDLDTVILK ALVKACKSHS RDAQDYLDEL KLAVAWDRVD IAKSEIFNGD VEWKSCDLEE VMTD ALVSN KPDFVRLFVD SGADMAEFLT YGRLQQLYHS VSPKSLLFEL LERKHEEGRL TLAGLGAQQT RELPVGLPAF SLHEV SRVL KDFLHDACRG FYQDGRRMEE RGPPKRPAGQ KWLPDLSRKS EDPWRDLFLW AVLQNRYEMA TYFWAMGREG VAAALA ACK IIKEMSHLEK EAEVARTMRE AKYEQLALDL FSECYSNSED RAFALLVRRN HSWSRTTCLH LATEADAKAF FAHDGVQ AF LTKIWWGDMA TGTPILRLLG AFTCPALIYT NLISFSEDAP QRMDLEDLQE PDSLDMEKSF LCSHGGQLEK LTEAPRAP G DLGPQAAFLL TRWRKFWGAP VTVFLGNVVM YFAFLFLFSY VLLVDFRPPP QGPSGSEVTL YFWVFTLVLE EIRQGFFTN EDTRLVKKFT LYVEDNWNKC DMVAIFLFIV GVTCRMVPSV FEAGRTVLAI DFMVFTLRLI HIFAIHKQLG PKIIIVERMM KDVFFFLFF LSVWLVAYGV TTQALLHPHD GRLEWIFRRV LYRPYLQIFG QIPLDEIDEA RVNCSLHPLL LDSSASCPNL Y ANWLVILL LVTFLLVTNV LLMNLLIAMF SYTFQVVQGN ADMFWKFQRY HLIVEYHGRP ALAPPFILLS HLSLVLKQVF RK EAQHKQQ HLERDLPDPV DQKIITWETV QKENFLSTME KRRRDSEEEV LRKTAHRVDL IAKYIGGLRE QEKRIKCLES QAN YCMLLL SSMTDTLAPG GTYSSSQNCG RRSQPASARD REYLEAGLPH SDT

UniProtKB: Transient receptor potential cation channel subfamily M member 5

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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 / Cooling holder cryogen: NITROGEN
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 reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.2 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
FSC plot (resolution estimation)

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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
Output model

PDB-8sl8:
Cryo-EM structure of the rat TRPM5 channel in trace calcium, trace-1

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