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- EMDB-8118: Structure of TRPV1 determined in lipid nanodisc -

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Basic information

Entry
Database: EMDB / ID: EMD-8118
TitleStructure of TRPV1 determined in lipid nanodisc
Map dataTRPV1
Sample
  • Complex: TRPV1 ion channel in unliganded state
    • Protein or peptide: Transient receptor potential cation channel subfamily V member 1
  • Ligand: (4R,7S)-4-hydroxy-N,N,N-trimethyl-4,9-dioxo-7-[(pentanoyloxy)methyl]-3,5,8-trioxa-4lambda~5~-phosphatetradecan-1-aminium
  • Ligand: (2S)-1-{[(R)-hydroxy{[(1R,2R,3S,4S,5S,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}-3-(pentanoyloxy)propan-2-yl decanoate
  • Ligand: (2S)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(hexanoyloxy)propyl hexanoate
KeywordsTRP / ion channel / nanodisc / vanilloid / lipid / TRANSPORT PROTEIN
Function / homology
Function and homology information


response to capsazepine / negative regulation of establishment of blood-brain barrier / sensory perception of mechanical stimulus / peptide secretion / excitatory extracellular ligand-gated monoatomic ion channel activity / temperature-gated ion channel activity / cellular response to temperature stimulus / detection of chemical stimulus involved in sensory perception of pain / urinary bladder smooth muscle contraction / TRP channels ...response to capsazepine / negative regulation of establishment of blood-brain barrier / sensory perception of mechanical stimulus / peptide secretion / excitatory extracellular ligand-gated monoatomic ion channel activity / temperature-gated ion channel activity / cellular response to temperature stimulus / detection of chemical stimulus involved in sensory perception of pain / urinary bladder smooth muscle contraction / TRP channels / smooth muscle contraction involved in micturition / fever generation / thermoception / detection of temperature stimulus involved in thermoception / cellular response to acidic pH / response to pH / negative regulation of systemic arterial blood pressure / dendritic spine membrane / chloride channel regulator activity / glutamate secretion / monoatomic cation transmembrane transporter activity / negative regulation of heart rate / cellular response to ATP / ligand-gated monoatomic ion channel activity / response to pain / temperature homeostasis / cellular response to alkaloid / diet induced thermogenesis / cellular response to cytokine stimulus / intracellularly gated calcium channel activity / behavioral response to pain / detection of temperature stimulus involved in sensory perception of pain / negative regulation of mitochondrial membrane potential / calcium ion import across plasma membrane / monoatomic cation channel activity / extracellular ligand-gated monoatomic ion channel activity / sensory perception of pain / phosphatidylinositol binding / GABA-ergic synapse / phosphoprotein binding / microglial cell activation / cellular response to nerve growth factor stimulus / cellular response to growth factor stimulus / calcium ion transmembrane transport / calcium channel activity / lipid metabolic process / response to peptide hormone / calcium ion transport / positive regulation of nitric oxide biosynthetic process / transmembrane signaling receptor activity / sensory perception of taste / cellular response to tumor necrosis factor / cellular response to heat / response to heat / positive regulation of cytosolic calcium ion concentration / monoatomic ion transmembrane transport / protein homotetramerization / postsynaptic membrane / calmodulin binding / neuron projection / positive regulation of apoptotic process / external side of plasma membrane / neuronal cell body / dendrite / negative regulation of transcription by RNA polymerase II / ATP binding / metal ion binding / identical protein binding / membrane / plasma membrane
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 speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.28 Å
AuthorsGao Y / Cao E
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS047723 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R37NS065071 United States
National Institutes of Health/Office of the DirectorS10OD020054 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM098672 United States
CitationJournal: Nature / Year: 2016
Title: TRPV1 structures in nanodiscs reveal mechanisms of ligand and lipid action.
Authors: Yuan Gao / Erhu Cao / David Julius / Yifan Cheng /
Abstract: When integral membrane proteins are visualized in detergents or other artificial systems, an important layer of information is lost regarding lipid interactions and their effects on protein structure. ...When integral membrane proteins are visualized in detergents or other artificial systems, an important layer of information is lost regarding lipid interactions and their effects on protein structure. This is especially relevant to proteins for which lipids have both structural and regulatory roles. Here we demonstrate the power of combining electron cryo-microscopy with lipid nanodisc technology to ascertain the structure of the rat TRPV1 ion channel in a native bilayer environment. Using this approach, we determined the locations of annular and regulatory lipids and showed that specific phospholipid interactions enhance binding of a spider toxin to TRPV1 through formation of a tripartite complex. Furthermore, phosphatidylinositol lipids occupy the binding site for capsaicin and other vanilloid ligands, suggesting a mechanism whereby chemical or thermal stimuli elicit channel activation by promoting the release of bioactive lipids from a critical allosteric regulatory site.
History
DepositionMar 31, 2016-
Header (metadata) releaseMay 25, 2016-
Map releaseMay 25, 2016-
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: 4.3
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 4.3
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5irz
  • Surface level: 4.3
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8118.png

Downloads & links

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Map

FileDownload / File: emd_8118.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTRPV1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.22 Å/pix.
x 192 pix.
= 233.395 Å		1.22 Å/pix.
x 192 pix.
= 233.395 Å		1.22 Å/pix.
x 192 pix.
= 233.395 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2156 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 4.0 / Movie #1: 4.3
Minimum - Maximum-12.105636000000001 - 23.052073
Average (Standard dev.)-0.000000000307719 (±0.99999994)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 233.3952 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.21559895833331.21559895833331.2155989583333
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z233.395233.395233.395
α/β/γ90.00090.00090.000
start NX/NY/NZ-25-77-48
NX/NY/NZ899896
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS192192192
D min/max/mean-12.10623.052-0.000

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Supplemental data

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Half map: TRPV1, half map 1

Fileemd_8118_half_map_1.map
AnnotationTRPV1, half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: TRPV1, half map 2

Fileemd_8118_half_map_2.map
AnnotationTRPV1, half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : TRPV1 ion channel in unliganded state

EntireName: TRPV1 ion channel in unliganded state
Components
  • Complex: TRPV1 ion channel in unliganded state
    • Protein or peptide: Transient receptor potential cation channel subfamily V member 1
  • Ligand: (4R,7S)-4-hydroxy-N,N,N-trimethyl-4,9-dioxo-7-[(pentanoyloxy)methyl]-3,5,8-trioxa-4lambda~5~-phosphatetradecan-1-aminium
  • Ligand: (2S)-1-{[(R)-hydroxy{[(1R,2R,3S,4S,5S,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}-3-(pentanoyloxy)propan-2-yl decanoate
  • Ligand: (2S)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(hexanoyloxy)propyl hexanoate

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Supramolecule #1: TRPV1 ion channel in unliganded state

SupramoleculeName: TRPV1 ion channel in unliganded state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Rattus norvegicus (Norway rat)

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Macromolecule #1: Transient receptor potential cation channel subfamily V member 1

MacromoleculeName: Transient receptor potential cation channel subfamily V member 1
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 72.959297 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AMGSRLYDRR SIFDAVAQSN CQELESLLPF LQRSKKRLTD SEFKDPETGK TCLLKAMLNL HNGQNDTIAL LLDVARKTDS LKQFVNASY TDSYYKGQTA LHIAIERRNM TLVTLLVENG ADVQAAANGD FFKKTKGRPG FYFGELPLSL AACTNQLAIV K FLLQNSWQ ...String:
AMGSRLYDRR SIFDAVAQSN CQELESLLPF LQRSKKRLTD SEFKDPETGK TCLLKAMLNL HNGQNDTIAL LLDVARKTDS LKQFVNASY TDSYYKGQTA LHIAIERRNM TLVTLLVENG ADVQAAANGD FFKKTKGRPG FYFGELPLSL AACTNQLAIV K FLLQNSWQ PADISARDSV GNTVLHALVE VADNTVDNTK FVTSMYNEIL ILGAKLHPTL KLEEITNRKG LTPLALAASS GK IGVLAYI LQREIHEPEC RHLSRKFTEW AYGPVHSSLY DLSCIDTCEK NSVLEVIAYS SSETPNRHDM LLVEPLNRLL QDK WDRFVK RIFYFNFFVY CLYMIIFTAA AYYRPVEGLP PYKLKNTVGD YFRVTGEILS VSGGVYFFFR GIQYFLQRRP SLKS LFVDS YSEILFFVQS LFMLVSVVLY FSQRKEYVAS MVFSLAMGWT NMLYYTRGFQ QMGIYAVMIE KMILRDLCRF MFVYL VFLF GFSTAVVTLI EDGKYNSLYS TCLELFKFTI GMGDLEFTEN YDFKAVFIIL LLAYVILTYI LLLNMLIALM GETVNK IAQ ESKNIWKLQR AITILDTEKS FLKCMRKAFR SGKLLQVGFT PDGKDDYRWC FRVDEVNWTT WNTNVGIINE DPG

UniProtKB: Transient receptor potential cation channel subfamily V member 1, Transient receptor potential cation channel subfamily V member 1

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Macromolecule #2: (4R,7S)-4-hydroxy-N,N,N-trimethyl-4,9-dioxo-7-[(pentanoyloxy)meth...

MacromoleculeName: (4R,7S)-4-hydroxy-N,N,N-trimethyl-4,9-dioxo-7-[(pentanoyloxy)methyl]-3,5,8-trioxa-4lambda~5~-phosphatetradecan-1-aminium
type: ligand / ID: 2 / Number of copies: 4 / Formula: 6O8
Molecular weightTheoretical: 440.489 Da
Chemical component information

ChemComp-6O8:
(4R,7S)-4-hydroxy-N,N,N-trimethyl-4,9-dioxo-7-[(pentanoyloxy)methyl]-3,5,8-trioxa-4lambda~5~-phosphatetradecan-1-aminium

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Macromolecule #3: (2S)-1-{[(R)-hydroxy{[(1R,2R,3S,4S,5S,6S)-2,3,4,5,6-pentahydroxyc...

MacromoleculeName: (2S)-1-{[(R)-hydroxy{[(1R,2R,3S,4S,5S,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}-3-(pentanoyloxy)propan-2-yl decanoate
type: ligand / ID: 3 / Number of copies: 4 / Formula: 6ES
Molecular weightTheoretical: 572.58 Da
Chemical component information

ChemComp-6ES:
(2S)-1-{[(R)-hydroxy{[(1R,2R,3S,4S,5S,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}-3-(pentanoyloxy)propan-2-yl decanoate

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Macromolecule #4: (2S)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(hexanoylo...

MacromoleculeName: (2S)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(hexanoyloxy)propyl hexanoate
type: ligand / ID: 4 / Number of copies: 16 / Formula: 6OE
Molecular weightTheoretical: 411.428 Da
Chemical component information

ChemComp-6OE:
(2S)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(hexanoyloxy)propyl hexanoate

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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

Concentration0.5 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
150.0 mMNaClsodium chloride
2.0 mMC9H15O6PTCEP
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 12 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 290.0 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK III
Details: Blot for 6 seconds before plunging into liquid ethane (FEI VITROBOT MARK III)..
DetailsThis sample was monodisperse.

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Electron microscopy

MicroscopeFEI POLARA 300
TemperatureMin: 70.0 K / Max: 70.0 K
DetailsGrid screening was performed manually.
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-30 / Number grids imaged: 1 / Number real images: 1000 / Average exposure time: 6.0 sec. / Average electron dose: 41.0 e/Å2
Details: Images were collected in movie mode at 5 frames per second for 6 seconds.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 30.0 µm / Calibrated defocus max: 2.2 µm / Calibrated defocus min: 0.7000000000000001 µm / Calibrated magnification: 41132 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 31000
Sample stageSpecimen holder model: OTHER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

DetailsEach image stack was subjected to whole-frame motion correction followed by correction at the individual pixel level using program UcsfDfCorr.
Particle selectionNumber selected: 159193
Details: Initial manual particle picking and automatic particle picking were performed using SamViewer and several python scripts based on SPIDER.
Startup modelType of model: EMDB MAP
EMDB ID:

5778

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.3) / Number images used: 30689
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 1.3)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 1.3)
Final 3D classificationNumber classes: 6 / Avg.num./class: 25000 / Software - Name: RELION (ver. 1.3)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

3j5p


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: correlation coefficient
Output model

PDB-5irz:
Structure of TRPV1 determined in lipid nanodisc

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