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- EMDB-41866: TRPV1 in nanodisc bound with empty vanilloid binding pocket at 25C -

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Basic information

Entry
Database: EMDB / ID: EMD-41866
TitleTRPV1 in nanodisc bound with empty vanilloid binding pocket at 25C
Map data
Sample
  • Complex: TRPV1 in nanodisc with empty vanilloid binding pocket at 25C
    • Protein or peptide: Transient receptor potential cation channel subfamily V member 1
  • Ligand: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
  • Ligand: SODIUM ION
  • Ligand: water
KeywordsTRPV1 in nanodisc bound with empty vanilloid binding pocket at 25C / MEMBRANE PROTEIN
Function / homology
Function and homology information


response to capsazepine / negative regulation of establishment of blood-brain barrier / sensory perception of mechanical stimulus / excitatory extracellular ligand-gated monoatomic ion channel activity / peptide secretion / temperature-gated ion channel activity / detection of chemical stimulus involved in sensory perception of pain / cellular response to temperature stimulus / urinary bladder smooth muscle contraction / TRP channels ...response to capsazepine / negative regulation of establishment of blood-brain barrier / sensory perception of mechanical stimulus / excitatory extracellular ligand-gated monoatomic ion channel activity / peptide secretion / temperature-gated ion channel activity / detection of chemical stimulus involved in sensory perception of pain / cellular response to temperature stimulus / 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 / negative regulation of systemic arterial blood pressure / response to pH / dendritic spine membrane / chloride channel regulator activity / monoatomic cation transmembrane transporter activity / glutamate secretion / negative regulation of heart rate / cellular response to ATP / 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 / ligand-gated monoatomic ion channel activity / 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 / lipid metabolic process / calcium channel activity / calcium ion transmembrane transport / response to peptide hormone / calcium ion transport / transmembrane signaling receptor activity / positive regulation of nitric oxide biosynthetic process / sensory perception of taste / cellular response to tumor necrosis factor / cellular response to heat / positive regulation of cytosolic calcium ion concentration / response to heat / 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 / identical protein binding / membrane / metal ion binding / 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: 3.7 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_41866.png

Downloads & links

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Map

FileDownload / File: emd_41866.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.68 Å/pix.
x 416 pix.
= 282.88 Å		0.68 Å/pix.
x 416 pix.
= 282.88 Å		0.68 Å/pix.
x 416 pix.
= 282.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.68 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-1.4235631 - 2.7293098
Average (Standard dev.)0.0026347234 (±0.06828402)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions416416416
Spacing416416416
CellA=B=C: 282.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_41866_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_41866_half_map_2.map
Projections & Slices
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Sample components

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Entire : TRPV1 in nanodisc with empty vanilloid binding pocket at 25C

EntireName: TRPV1 in nanodisc with empty vanilloid binding pocket at 25C
Components
  • Complex: TRPV1 in nanodisc with empty vanilloid binding pocket at 25C
    • Protein or peptide: Transient receptor potential cation channel subfamily V member 1
  • Ligand: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
  • Ligand: SODIUM ION
  • Ligand: water

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Supramolecule #1: TRPV1 in nanodisc with empty vanilloid binding pocket at 25C

SupramoleculeName: TRPV1 in nanodisc with empty vanilloid binding pocket at 25C
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: 4 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 92.654172 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEQRASLDSE ESESPPQENS CLDPPDRDPN CKPPPVKPHI FTTRSRTRLF GKGDSEEASP LDCPYEEGGL ASCPIITVSS VLTIQRPGD GPASVRPSSQ DSVSAGEKPP RLYDRRSIFD AVAQSNCQEL ESLLPFLQRS KKRLTDSEFK DPETGKTCLL K AMLNLHNG ...String:
MEQRASLDSE ESESPPQENS CLDPPDRDPN CKPPPVKPHI FTTRSRTRLF GKGDSEEASP LDCPYEEGGL ASCPIITVSS VLTIQRPGD GPASVRPSSQ DSVSAGEKPP RLYDRRSIFD AVAQSNCQEL ESLLPFLQRS KKRLTDSEFK DPETGKTCLL K AMLNLHNG QNDTIALLLD VARKTDSLKQ FVNASYTDSY YKGQTALHIA IERRNMTLVT LLVENGADVQ AAANGDFFKK TK GRPGFYF GELPLSLAAC TNQLAIVKFL LQNSWQPADI SARDSVGNTV LHALVEVADN TVDNTKFVTS MYNEILILGA KLH PTLKLE EITNRKGLTP LALAASSGKI GVLAYILQRE IHEPECRHLS RKFTEWAYGP VHSSLYDLSC IDTCEKNSVL EVIA YSSSE TPNRHDMLLV EPLNRLLQDK WDRFVKRIFY FNFFVYCLYM IIFTAAAYYR PVEGLPPYKL KNTVGDYFRV TGEIL SVSG GVYFFFRGIQ YFLQRRPSLK SLFVDSYSEI LFFVQSLFML VSVVLYFSQR KEYVASMVFS LAMGWTNMLY YTRGFQ QMG IYAVMIEKMI LRDLCRFMFV YLVFLFGFST AVVTLIEDGK YNSLYSTCLE LFKFTIGMGD LEFTENYDFK AVFIILL LA YVILTYILLL NMLIALMGET VNKIAQESKN IWKLQRAITI LDTEKSFLKC MRKAFRSGKL LQVGFTPDGK DDYRWCFR V DEVNWTTWNT NVGIINEDPG NCEGVKRTLS FSLRSGRVSG RNWKNFALVP LLRDASTRDR HATQQEEVQL KHYTGSLKP EDAEVFKDSM VPGEK

UniProtKB: Transient receptor potential cation channel subfamily V member 1

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Macromolecule #2: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE

MacromoleculeName: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / type: ligand / ID: 2 / Number of copies: 4 / Formula: 3PH
Molecular weightTheoretical: 704.998 Da
Chemical component information

ChemComp-3PH:
1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE

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Macromolecule #3: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 3 / Number of copies: 1
Molecular weightTheoretical: 22.99 Da

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 4 / 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: 60.0 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: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 39183
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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