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- EMDB-41855: TRPV1 in nanodisc bound with PI-Br4 bound in Conformation 1 (monomer) -

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Basic information

Entry
Database: EMDB / ID: EMD-41855
TitleTRPV1 in nanodisc bound with PI-Br4 bound in Conformation 1 (monomer)
Map dataTRPV1 monomer bound with PI-Br4 in Conformation 1
Sample
  • Complex: TRPV1 in nanodisc bound with PI-Br4 in Conformation 1 (monomer)
    • Protein or peptide: Transient receptor potential cation channel subfamily V member 1
  • Ligand: (2S)-2-[(9,10-dibromooctadecanoyl)oxy]-3-{[(S)-hydroxy{[(1S,2R,3R,4S,5S,6R)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propyl (9R,10S)-9,10-dibromooctadecanoate
  • Ligand: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: SODIUM ION
  • Ligand: water
KeywordsTRPV1 in nanodisc bound with PI-Br4 bound in Conformation 1 (monomer) / MEMBRANE PROTEIN
Function / homology
Function and homology information


negative regulation of iodide transmembrane transport / positive regulation of membrane depolarization / negative regulation of establishment of blood-brain barrier / response to capsazepine / sensory perception of mechanical stimulus / peptide secretion / cellular response to temperature stimulus / positive regulation of sensory perception of pain / temperature-gated ion channel activity / detection of chemical stimulus involved in sensory perception of pain ...negative regulation of iodide transmembrane transport / positive regulation of membrane depolarization / negative regulation of establishment of blood-brain barrier / response to capsazepine / sensory perception of mechanical stimulus / peptide secretion / cellular response to temperature stimulus / positive regulation of sensory perception of pain / temperature-gated ion channel activity / detection of chemical stimulus involved in sensory perception of pain / positive regulation of renal sodium excretion / negative regulation of axon regeneration / TRP channels / positive regulation of cardiac muscle cell differentiation / smooth muscle contraction involved in micturition / fever generation / detection of temperature stimulus involved in thermoception / thermoception / urinary bladder smooth muscle contraction / response to pH / monoatomic cation transmembrane transporter activity / glutamate secretion / negative regulation of systemic arterial blood pressure / dendritic spine membrane / positive regulation of urine volume / excitatory extracellular ligand-gated monoatomic ion channel activity / negative regulation of heart rate / response to acidic pH / response to pain / diet induced thermogenesis / cellular response to alkaloid / temperature homeostasis / cellular response to cytokine stimulus / cellular response to ATP / intracellularly gated calcium channel activity / detection of temperature stimulus involved in sensory perception of pain / negative regulation of mitochondrial membrane potential / behavioral response to pain / calcium ion import across plasma membrane / positive regulation of vasoconstriction / monoatomic ion channel activity / ligand-gated monoatomic ion channel activity / monoatomic cation channel activity / cellular response to acidic pH / extracellular ligand-gated monoatomic ion channel activity / phosphatidylinositol binding / sensory perception of pain / axon terminus / positive regulation of excitatory postsynaptic potential / sarcoplasmic reticulum / lipid metabolic process / phosphoprotein binding / microglial cell activation / cellular response to nerve growth factor stimulus / response to peptide hormone / cellular response to growth factor stimulus / GABA-ergic synapse / calcium ion transmembrane transport / cellular response to tumor necrosis factor / calcium channel activity / positive regulation of nitric oxide biosynthetic process / calcium ion transport / transmembrane signaling receptor activity / cellular response to heat / sensory perception of taste / response to heat / positive regulation of cytosolic calcium ion concentration / monoatomic ion transmembrane transport / protein homotetramerization / calmodulin binding / postsynaptic membrane / 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 / membrane / metal ion binding / identical protein binding / nucleus / 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: 2.3 Å
AuthorsArnold WR / Julius D / Cheng Y
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nat Struct Mol Biol / Year: 2024
Title: Structural basis of TRPV1 modulation by endogenous bioactive lipids.
Authors: William R Arnold / Adamo Mancino / Frank R Moss / Adam Frost / David Julius / Yifan Cheng /
Abstract: TRP ion channels are modulated by phosphoinositide lipids, but the underlying structural mechanisms remain unclear. The capsaicin- and heat-activated receptor, TRPV1, has served as a model for ...TRP ion channels are modulated by phosphoinositide lipids, but the underlying structural mechanisms remain unclear. The capsaicin- and heat-activated receptor, TRPV1, has served as a model for deciphering lipid modulation, which is relevant to understanding how pro-algesic agents enhance channel activity in the setting of inflammatory pain. Identification of a pocket within the TRPV1 transmembrane core has provided initial clues as to how phosphoinositide lipids bind to and regulate the channel. Here we show that this regulatory pocket in rat TRPV1 can accommodate diverse lipid species, including the inflammatory lipid lysophosphatidic acid, whose actions are determined by their specific modes of binding. Furthermore, we show that an empty-pocket channel lacking an endogenous phosphoinositide lipid assumes an agonist-like state, even at low temperature, substantiating the concept that phosphoinositide lipids serve as negative TRPV1 modulators whose ejection from the binding pocket is a critical step toward activation by thermal or chemical stimuli.
History
DepositionSep 7, 2023-
Header (metadata) releaseMay 8, 2024-
Map releaseMay 8, 2024-
UpdateOct 2, 2024-
Current statusOct 2, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41855.png

Downloads & links

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Map

FileDownload / File: emd_41855.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTRPV1 monomer bound with PI-Br4 in Conformation 1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.64 Å/pix.
x 416 pix.
= 267.904 Å		0.64 Å/pix.
x 416 pix.
= 267.904 Å		0.64 Å/pix.
x 416 pix.
= 267.904 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.644 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.003
Minimum - Maximum-0.05458766 - 0.14285606
Average (Standard dev.)0.0000053687722 (±0.0014632443)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions416416416
Spacing416416416
CellA=B=C: 267.904 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: TRPV1 monomer bound with PI-Br4 in Conformation 1 half map 2

Fileemd_41855_half_map_1.map
AnnotationTRPV1 monomer bound with PI-Br4 in Conformation 1 half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: TRPV1 monomer bound with PI-Br4 in Conformation 1 half map 1

Fileemd_41855_half_map_2.map
AnnotationTRPV1 monomer bound with PI-Br4 in Conformation 1 half map 1
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 in nanodisc bound with PI-Br4 in Conformation 1 (monomer)

EntireName: TRPV1 in nanodisc bound with PI-Br4 in Conformation 1 (monomer)
Components
  • Complex: TRPV1 in nanodisc bound with PI-Br4 in Conformation 1 (monomer)
    • Protein or peptide: Transient receptor potential cation channel subfamily V member 1
  • Ligand: (2S)-2-[(9,10-dibromooctadecanoyl)oxy]-3-{[(S)-hydroxy{[(1S,2R,3R,4S,5S,6R)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propyl (9R,10S)-9,10-dibromooctadecanoate
  • Ligand: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: SODIUM ION
  • Ligand: water

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Supramolecule #1: TRPV1 in nanodisc bound with PI-Br4 in Conformation 1 (monomer)

SupramoleculeName: TRPV1 in nanodisc bound with PI-Br4 in Conformation 1 (monomer)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 688 KDa

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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: 2 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 72.888227 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGSRLYDRRS IFDAVAQSNC QELESLLPFL QRSKKRLTDS EFKDPETGKT CLLKAMLNLH NGQNDTIALL LDVARKTDSL KQFVNASYT DSYYKGQTAL HIAIERRNMT LVTLLVENGA DVQAAANGDF FKKTKGRPGF YFGELPLSLA ACTNQLAIVK F LLQNSWQP ...String:
MGSRLYDRRS IFDAVAQSNC QELESLLPFL QRSKKRLTDS EFKDPETGKT CLLKAMLNLH NGQNDTIALL LDVARKTDSL KQFVNASYT DSYYKGQTAL HIAIERRNMT LVTLLVENGA DVQAAANGDF FKKTKGRPGF YFGELPLSLA ACTNQLAIVK F LLQNSWQP ADISARDSVG NTVLHALVEV ADNTVDNTKF VTSMYNEILI LGAKLHPTLK LEEITNRKGL TPLALAASSG KI GVLAYIL QREIHEPECR HLSRKFTEWA YGPVHSSLYD LSCIDTCEKN SVLEVIAYSS SETPNRHDML LVEPLNRLLQ DKW DRFVKR IFYFNFFVYC LYMIIFTAAA YYRPVEGLPP YKLKNTVGDY FRVTGEILSV SGGVYFFFRG IQYFLQRRPS LKSL FVDSY SEILFFVQSL FMLVSVVLYF SQRKEYVASM VFSLAMGWTN MLYYTRGFQQ MGIYAVMIEK MILRDLCRFM FVYLV FLFG FSTAVVTLIE DGKYNSLYST CLELFKFTIG MGDLEFTENY DFKAVFIILL LAYVILTYIL LLNMLIALMG ETVNKI AQE SKNIWKLQRA ITILDTEKSF LKCMRKAFRS GKLLQVGFTP DGKDDYRWCF RVDEVNWTTW NTNVGIINED PG

UniProtKB: Transient receptor potential cation channel subfamily V member 1

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Macromolecule #2: (2S)-2-[(9,10-dibromooctadecanoyl)oxy]-3-{[(S)-hydroxy{[(1S,2R,3R...

MacromoleculeName: (2S)-2-[(9,10-dibromooctadecanoyl)oxy]-3-{[(S)-hydroxy{[(1S,2R,3R,4S,5S,6R)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propyl (9R,10S)-9,10-dibromooctadecanoate
type: ligand / ID: 2 / Number of copies: 1 / Formula: VPN
Molecular weightTheoretical: 1.182722 KDa

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Macromolecule #3: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 3 / Number of copies: 1 / Formula: PCW
Molecular weightTheoretical: 787.121 Da
Chemical component information

ChemComp-PCW:
1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / DOPC, phospholipid*YM

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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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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 12 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration2.1 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 47.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / 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

Startup modelType of model: EMDB MAP
EMDB ID:

8118

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 715030
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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