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- EMDB-23856: Mouse TRPV3 in cNW11 nanodiscs, closed state at 4 degrees Celsius -

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Basic information

Entry
Database: EMDB / ID: EMD-23856
TitleMouse TRPV3 in cNW11 nanodiscs, closed state at 4 degrees Celsius
Map dataTRPV3 in cNW11 nanodiscs, closed state at 4 degrees Celsius
Sample
  • Complex: Transient receptor potential cation channel subfamily V member 3
    • 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: SODIUM ION
KeywordsTransient Receptor Potential V Family Member 3 / TRP channel / TRPV3 / closed state at 4 degrees Celsius / cNW11 / 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: 3.42 Å
AuthorsNeuberger A / Nadezhdin KD
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA206573 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01 NS083660 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01 NS107253 United States
National Science Foundation (NSF, United States)1818086 United States
CitationJournal: Nat Struct Mol Biol / Year: 2021
Title: Structural mechanism of heat-induced opening of a temperature-sensitive TRP channel.
Authors: Kirill D Nadezhdin / Arthur Neuberger / Yuri A Trofimov / Nikolay A Krylov / Viktor Sinica / Nikita Kupko / Viktorie Vlachova / Eleonora Zakharian / Roman G Efremov / Alexander I Sobolevsky /
Abstract: Numerous physiological functions rely on distinguishing temperature through temperature-sensitive transient receptor potential channels (thermo-TRPs). Although the function of thermo-TRPs has been ...Numerous physiological functions rely on distinguishing temperature through temperature-sensitive transient receptor potential channels (thermo-TRPs). Although the function of thermo-TRPs has been studied extensively, structural determination of their heat- and cold-activated states has remained a challenge. Here, we present cryo-EM structures of the nanodisc-reconstituted wild-type mouse TRPV3 in three distinct conformations: closed, heat-activated sensitized and open states. The heat-induced transformations of TRPV3 are accompanied by changes in the secondary structure of the S2-S3 linker and the N and C termini and represent a conformational wave that links these parts of the protein to a lipid occupying the vanilloid binding site. State-dependent differences in the behavior of bound lipids suggest their active role in thermo-TRP temperature-dependent gating. Our structural data, supported by physiological recordings and molecular dynamics simulations, provide an insight for understanding the molecular mechanism of temperature sensing.
History
DepositionApr 17, 2021-
Header (metadata) releaseJul 21, 2021-
Map releaseJul 21, 2021-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0278
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0278
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7mim
  • Surface level: 0.0278
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23856.png

Downloads & links

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Map

FileDownload / File: emd_23856.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTRPV3 in cNW11 nanodiscs, closed state at 4 degrees Celsius
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 256 pix.
= 282.88 Å		1.11 Å/pix.
x 256 pix.
= 282.88 Å		1.11 Å/pix.
x 256 pix.
= 282.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.105 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0278 / Movie #1: 0.0278
Minimum - Maximum-0.11542511 - 0.1845825
Average (Standard dev.)0.0004168922 (±0.006220977)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 282.88 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1051.1051.105
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z282.880282.880282.880
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.1150.1850.000

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Supplemental data

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Sample components

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Entire : Transient receptor potential cation channel subfamily V member 3

EntireName: Transient receptor potential cation channel subfamily V member 3
Components
  • Complex: Transient receptor potential cation channel subfamily V member 3
    • 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: SODIUM ION

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Supramolecule #1: Transient receptor potential cation channel subfamily V member 3

SupramoleculeName: Transient receptor potential cation channel subfamily V member 3
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 924.7 KDa

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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: 92.630695 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MNAHSKEMAP LMGKRTTAPG GNPVVLTEKR PADLTPTKKS AHFFLEIEGF EPNPTVTKTS PPIFSKPMDS NIRQCLSGNC DDMDSPQSP QDDVTETPSN PNSPSANLAK EEQRQKKKRL KKRIFAAVSE GCVEELRELL QDLQDLCRRR RGLDVPDFLM H KLTASDTG ...String:
MNAHSKEMAP LMGKRTTAPG GNPVVLTEKR PADLTPTKKS AHFFLEIEGF EPNPTVTKTS PPIFSKPMDS NIRQCLSGNC DDMDSPQSP QDDVTETPSN PNSPSANLAK EEQRQKKKRL KKRIFAAVSE GCVEELRELL QDLQDLCRRR RGLDVPDFLM H KLTASDTG KTCLMKALLN INPNTKEIVR ILLAFAEEND ILDRFINAEY TEEAYEGQTA LNIAIERRQG DITAVLIAAG AD VNAHAKG VFFNPKYQHE GFYFGETPLA LAACTNQPEI VQLLMENEQT DITSQDSRGN NILHALVTVA EDFKTQNDFV KRM YDMILL RSGNWELETM RNNDGLTPLQ LAAKMGKAEI LKYILSREIK EKPLRSLSRK FTDWAYGPVS SSLYDLTNVD TTTD NSVLE IIVYNTNIDN RHEMLTLEPL HTLLHTKWKK FAKYMFFLSF CFYFFYNITL TLVSYYRPRE DEDLPHPLAL THKMS WLQL LGRMFVLIWA TCISVKEGIA IFLLRPSDLQ SILSDAWFHF VFFVQAVLVI LSVFLYLFAY KEYLACLVLA MALGWA NML YYTRGFQSMG MYSVMIQKVI LHDVLKFLFV YILFLLGFGV ALASLIEKCS KDKKDCSSYG SFSDAVLELF KLTIGLG DL NIQQNSTYPI LFLFLLITYV ILTFVLLLNM LIALMGETVE NVSKESERIW RLQRARTILE FEKMLPEWLR SRFRMGEL C KVADEDFRLC LRINEVKWTE WKTHVSFLNE DPGPIRRTAD LNKIQDSSRS NSKTTLYAFD ELDEFPETSV LVPRGSAAA WSHPQFEK

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: 36 / 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: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 3 / Number of copies: 4
Molecular weightTheoretical: 22.99 Da

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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

Concentration2.4 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
20.0 mMtris(hydroxymethyl)aminomethane
1.0 mMbeta-Mercaptoethanol
4.0 mMEGTA
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 10878 / Average exposure time: 2.0 sec. / Average electron dose: 51.07 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: -2.0 µm / Nominal defocus min: -0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 10151026
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.42 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 159698
Initial angle assignmentType: OTHER / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: OTHER / Software - Name: RELION (ver. 3.1)
Final 3D classificationSoftware - Name: RELION (ver. 3.1)

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Atomic model buiding 1

RefinementSpace: REAL
Output model

PDB-7mim:
Mouse TRPV3 in cNW11 nanodiscs, closed state at 4 degrees Celsius

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