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- EMDB-0882: cryo-EM structure of TRPV3 in lipid nanodisc -

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Basic information

Entry
Database: EMDB / ID: EMD-0882
Titlecryo-EM structure of TRPV3 in lipid nanodisc
Map data
Sample
  • Organelle or cellular component: TRPV3
    • Protein or peptide: Transient receptor potential cation channel subfamily V member 3
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: DIUNDECYL PHOSPHATIDYL CHOLINE
KeywordsTRP channel / TRPV family / TRPV3 / nanodisc / MEMBRANE PROTEIN
Function / homology
Function and homology information


negative regulation of hair cycle / TRP channels / response to temperature stimulus / positive regulation of calcium ion import / monoatomic ion channel activity / monoatomic cation channel activity / calcium channel activity / lysosome / receptor complex / membrane ...negative regulation of hair cycle / TRP channels / response to temperature stimulus / positive regulation of calcium ion import / monoatomic ion channel activity / monoatomic cation channel activity / calcium channel activity / lysosome / receptor complex / membrane / plasma membrane / cytoplasm
Similarity search - Function
Transient receptor potential cation channel subfamily V member 1-4 / Transient receptor potential cation channel subfamily V / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Transient receptor potential cation channel subfamily V member 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsShimada H / Kusakizako T
CitationJournal: Nat Struct Mol Biol / Year: 2020
Title: The structure of lipid nanodisc-reconstituted TRPV3 reveals the gating mechanism.
Authors: Hiroto Shimada / Tsukasa Kusakizako / T H Dung Nguyen / Tomohiro Nishizawa / Tomoya Hino / Makoto Tominaga / Osamu Nureki /
Abstract: Transient receptor potential vanilloid subfamily member 3 (TRPV3) is a temperature-sensitive cation channel. Previous cryo-EM analyses of TRPV3 in detergent micelles or amphipol proposed that the ...Transient receptor potential vanilloid subfamily member 3 (TRPV3) is a temperature-sensitive cation channel. Previous cryo-EM analyses of TRPV3 in detergent micelles or amphipol proposed that the lower gate opens by α-to-π helical transitions of the nearby S6 helix. However, it remains unclear how physiological lipids are involved in the TRPV3 activation. Here we determined the apo state structure of mouse (Mus musculus) TRPV3 in a lipid nanodisc at 3.3 Å resolution. The structure revealed that lipids bound to the pore domain stabilize the selectivity filter in the narrow state, suggesting that the selectivity filter of TRPV3 affects cation permeation. When the lower gate is closed in nanodisc-reconstituted TRPV3, the S6 helix adopts the π-helical conformation without agonist- or heat-sensitization, potentially stabilized by putative intra-subunit hydrogen bonds and lipid binding. Our findings provide insights into the lipid-associated gating mechanism of TRPV3.
History
DepositionDec 5, 2019-
Header (metadata) releaseJun 24, 2020-
Map releaseJun 24, 2020-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6lgp
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0882.png

Downloads & links

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Map

FileDownload / File: emd_0882.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.45 Å/pix.
x 160 pix.
= 232. Å		1.45 Å/pix.
x 160 pix.
= 232. Å		1.45 Å/pix.
x 160 pix.
= 232. Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.45 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035 / Movie #1: 0.05
Minimum - Maximum-0.23704885 - 0.44331542
Average (Standard dev.)0.0011602396 (±0.015125863)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 232.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.451.451.45
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z232.000232.000232.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-0.2370.4430.001

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Supplemental data

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Mask #1

Fileemd_0882_msk_1.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Half map: #2

Fileemd_0882_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_0882_half_map_2.map
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Sample components

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Entire : TRPV3

EntireName: TRPV3
Components
  • Organelle or cellular component: TRPV3
    • Protein or peptide: Transient receptor potential cation channel subfamily V member 3
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: DIUNDECYL PHOSPHATIDYL CHOLINE

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Supramolecule #1: TRPV3

SupramoleculeName: TRPV3 / type: organelle_or_cellular_component / 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 V member 3

MacromoleculeName: Transient receptor potential cation channel subfamily V member 3
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 73.949867 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: RLKKRIFAAV SEGCVEELRE LLQDLQDLCR RRRGLDVPDF LMHKLTASDT GKTCLMKALL NINPNTKEIV RILLAFAEEN DILDRFINA EYTEEAYEGQ TALNIAIERR QGDITAVLIA AGADVNAHAK GVFFNPKYQH EGFYFGETPL ALAACTNQPE I VQLLMENE ...String:
RLKKRIFAAV SEGCVEELRE LLQDLQDLCR RRRGLDVPDF LMHKLTASDT GKTCLMKALL NINPNTKEIV RILLAFAEEN DILDRFINA EYTEEAYEGQ TALNIAIERR QGDITAVLIA AGADVNAHAK GVFFNPKYQH EGFYFGETPL ALAACTNQPE I VQLLMENE QTDITSQDSR GNNILHALVT VAEDFKTQND FVKRMYDMIL LRSGNWELET MRNNDGLTPL QLAAKMGKAE IL KYILSRE IKEKPLRSLS RKFTDWAYGP VSSSLYDLTN VDTTTDNSVL EIIVYNTNID NRHEMLTLEP LHTLLHTKWK KFA KYMFFL SFCFYFFYNI TLTLVSYYRP REDEDLPHPL ALTHKMSWLQ LLGRMFVLIW ATCISVKEGI AIFLLRPSDL QSIL SDAWF HFVFFVQAVL VILSVFLYLF AYKEYLACLV LAMALGWANM LYYTRGFQSM GMYSVMIQKV ILHDVLKFLF VYILF LLGF GVALASLIEK CSKDKKDCSS YGSFSDAVLE LFKLTIGLGD LNIQQNSTYP ILFLFLLITY VILTFVLLLN MLIALM GET VENVSKESER IWRLQRARTI LEFEKMLPEW LRSRFRMGEL CKVADEDFRL CLRINEVKWT EWKTHVSFLN EDPGPI

UniProtKB: Transient receptor potential cation channel subfamily V member 3

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Macromolecule #2: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...

MacromoleculeName: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
type: ligand / ID: 2 / Number of copies: 16 / Formula: POV
Molecular weightTheoretical: 760.076 Da
Chemical component information

ChemComp-POV:
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / phospholipid*YM

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Macromolecule #3: DIUNDECYL PHOSPHATIDYL CHOLINE

MacromoleculeName: DIUNDECYL PHOSPHATIDYL CHOLINE / type: ligand / ID: 3 / Number of copies: 12 / Formula: PLC
Molecular weightTheoretical: 622.834 Da
Chemical component information

ChemComp-PLC:
DIUNDECYL PHOSPHATIDYL CHOLINE / phospholipid*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

Concentration2.0 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER/RHODIUM / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 279 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: FEI FALCON III (4k x 4k) / #0 - Average electron dose: 50.0 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: FEI FALCON III (4k x 4k) / #1 - Average electron dose: 50.0 e/Å2 / #2 - Image recording ID: 3 / #2 - Film or detector model: FEI FALCON III (4k x 4k) / #2 - Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Image recording ID1
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6dvw

Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 106947
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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