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- EMDB-23493: Structure of squirrel TRPV1 in complex with capsaicin -

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Basic information

Entry
Database: EMDB / ID: EMD-23493
TitleStructure of squirrel TRPV1 in complex with capsaicin
Map data
Sample
  • Complex: sample 1
    • Protein or peptide: Osm-9-like TRP channel 1
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: (6E)-N-(4-hydroxy-3-methoxybenzyl)-8-methylnon-6-enamide
  • Ligand: SODIUM ION
KeywordsTransient Receptor Potential V Family Member 1 / TRP channel / TRPV1 full length / TRPV1 wild type / capsaicin / MEMBRANE PROTEIN
Function / homology
Function and homology information


response to capsazepine / sensory perception of mechanical stimulus / peptide secretion / temperature-gated ion channel activity / detection of chemical stimulus involved in sensory perception of pain / smooth muscle contraction involved in micturition / fever generation / detection of temperature stimulus involved in thermoception / cellular response to acidic pH / dendritic spine membrane ...response to capsazepine / sensory perception of mechanical stimulus / peptide secretion / temperature-gated ion channel activity / detection of chemical stimulus involved in sensory perception of pain / smooth muscle contraction involved in micturition / fever generation / detection of temperature stimulus involved in thermoception / cellular response to acidic pH / dendritic spine membrane / diet induced thermogenesis / detection of temperature stimulus involved in sensory perception of pain / behavioral response to pain / calcium ion import across plasma membrane / extracellular ligand-gated monoatomic ion channel activity / phosphoprotein binding / GABA-ergic synapse / calcium channel activity / lipid metabolic process / sensory perception of taste / cellular response to heat / postsynaptic membrane / calmodulin binding / negative regulation of transcription by RNA polymerase II / ATP binding / metal ion binding
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 1
Similarity search - Component
Biological speciesHomo sapiens (human) / Ictidomys tridecemlineatus (thirteen-lined ground squirrel)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.81 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 Commun / Year: 2021
Title: Extracellular cap domain is an essential component of the TRPV1 gating mechanism.
Authors: Kirill D Nadezhdin / Arthur Neuberger / Yury A Nikolaev / Lyle A Murphy / Elena O Gracheva / Sviatoslav N Bagriantsev / Alexander I Sobolevsky /
Abstract: Transient receptor potential (TRP) channels are polymodal molecular sensors involved in numerous physiological processes and implicated in a variety of human diseases. Several structures of the ...Transient receptor potential (TRP) channels are polymodal molecular sensors involved in numerous physiological processes and implicated in a variety of human diseases. Several structures of the founding member of the TRP channel family, TRPV1, are available, all of which were determined for the protein missing the N- and C-termini and the extracellular S5-P-loop. Here, we present structures of the full-length thirteen-lined ground squirrel TRPV1 solved by cryo-EM. Our structures resolve the extracellular cap domain formed by the S5-P-loops and the C-terminus that wraps around the three-stranded β-sheet connecting elements of the TRPV1 intracellular skirt. The cap domain forms a dome above the pore's extracellular entrance, with four portals leading to the ion conductance pathway. Deletion of the cap increases the TRPV1 average conductance, reduces the open probability and affects ion selectivity. Our data show that both the termini and the cap domain are critical determinants of TRPV1 function.
History
DepositionFeb 15, 2021-
Header (metadata) releaseApr 21, 2021-
Map releaseApr 21, 2021-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.395
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.395
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7lr0
  • Surface level: 0.395
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23493.png

Downloads & links

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Map

FileDownload / File: emd_23493.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 256 pix.
= 212.48 Å		0.83 Å/pix.
x 256 pix.
= 212.48 Å		0.83 Å/pix.
x 256 pix.
= 212.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.395 / Movie #1: 0.395
Minimum - Maximum-1.5680679 - 2.03379
Average (Standard dev.)0.015161309 (±0.09500724)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 212.48 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.830.830.83
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z212.480212.480212.480
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-1.5682.0340.015

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Supplemental data

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Sample components

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Entire : sample 1

EntireName: sample 1
Components
  • Complex: sample 1
    • Protein or peptide: Osm-9-like TRP channel 1
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: (6E)-N-(4-hydroxy-3-methoxybenzyl)-8-methylnon-6-enamide
  • Ligand: SODIUM ION

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Supramolecule #1: sample 1

SupramoleculeName: sample 1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Osm-9-like TRP channel 1

MacromoleculeName: Osm-9-like TRP channel 1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Ictidomys tridecemlineatus (thirteen-lined ground squirrel)
Molecular weightTheoretical: 95.902781 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKKWANLDSG ESEDPPHEDS CPDPPDGDPN SKQSPAKPHI FSTTKSRTRL FGKGDSEEAS PMDCSYEEGE LASCPTITVS SVVIIQRPG DALTCARQLS QDSVSAGAEK PLKLYDRRSI FDAVAQNNCQ ELESLLPFLQ KSRKRLTDSE FKDPETGKTC L LKAMLNLH ...String:
MKKWANLDSG ESEDPPHEDS CPDPPDGDPN SKQSPAKPHI FSTTKSRTRL FGKGDSEEAS PMDCSYEEGE LASCPTITVS SVVIIQRPG DALTCARQLS QDSVSAGAEK PLKLYDRRSI FDAVAQNNCQ ELESLLPFLQ KSRKRLTDSE FKDPETGKTC L LKAMLNLH NGQNDTISLL LDIARQTDSL KEFVNASYTD SYYKGQTALH IAIERRNMAL VTLLVENGAD VQAAANGDFF KK TKGRPGF YFGELPLSLA ACTNQLAIVK FLLQNSWQPA DISARDSVGN TVLHALVEVA DNTADNTKFV TSMYNEILIL GAK LHPTLK LEELINKKGL TPLALAASSG KIGVLAYILQ REIQEPECRH LSRKFTEWAY GPVHSSLYDL SCIDTCEKNS VLEV IAYSS SETPNRHDML LVEPLNRLLQ DKWDRFVKRI FYFNFFVYCL YMIVFTTAAY YRPVDGLPPY KLKNTVGDYF RVTGE ILSV SGGVYFFLRG IQYFLQRRPS MKTLFVDSYS EMLFFVQSLF MLGSVVLYFS HRKEYVASMV FSLAMGWTNM LYYTRG FQQ MGIYAVMIEK MILRDLCRFM FVYLVFLFGF STAVVTLIED GKNYSEPAEY TSHRWRAPGC RPPDSYNSLY STCLELF KF TIGMGDLEFT ENYDFKAVFI ILLLAYVILT YILLLNMLIA LMGETVNKIA QESKNIWKLQ RAITILDTEK SFLKCMRK A FRSGKLLQVG YTPDGKDDYR WCFRVDEVNW TTWNTNVGII NEDPGNCEGV KRTLSFSLRS GRVSGRNWRN FALVPLLRD ASTRDRHHAQ PEEVHLKHFA GSLKPEDAEV FKDSMAPGEK LPVR

UniProtKB: Transient receptor potential cation channel subfamily V member 1

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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: 28 / 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: (6E)-N-(4-hydroxy-3-methoxybenzyl)-8-methylnon-6-enamide

MacromoleculeName: (6E)-N-(4-hydroxy-3-methoxybenzyl)-8-methylnon-6-enamide
type: ligand / ID: 3 / Number of copies: 4 / Formula: 4DY
Molecular weightTheoretical: 305.412 Da
Chemical component information

ChemComp-4DY:
(6E)-N-(4-hydroxy-3-methoxybenzyl)-8-methylnon-6-enamide

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Macromolecule #4: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 4 / Number of copies: 1
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
0.01 %glyco-diosgenin (GDN)
1.0 mMbeta-Mercaptoethanol
300.0 uMcapsaicin
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Slit width: 30 eV
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: 9453 / Average exposure time: 2.5 sec. / Average electron dose: 58.5 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: -2.5 µm / Nominal defocus min: -1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2013743
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.81 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.15) / Number images used: 62014
Initial angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 2.15)
Final angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 2.15)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 2.15)

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Atomic model buiding 1

RefinementSpace: REAL
Output model

PDB-7lr0:
Structure of squirrel TRPV1 in complex with capsaicin

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