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- PDB-7lqy: Structure of squirrel TRPV1 in apo state -

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Basic information

Entry
Database: PDB / ID: 7lqy
TitleStructure of squirrel TRPV1 in apo state
ComponentsOsm-9-like TRP channel 1
KeywordsMEMBRANE PROTEIN / Transient Receptor Potential V Family Member 1 / TRP channel / TRPV1 full length / TRPV1 wild type
Function / homology
Function and homology information


temperature-gated ion channel activity / response to capsazepine / sensory perception of mechanical stimulus / peptide secretion / detection of chemical stimulus involved in sensory perception of pain / smooth muscle contraction involved in micturition / cellular response to acidic pH / fever generation / detection of temperature stimulus involved in thermoception / dendritic spine membrane ...temperature-gated ion channel activity / response to capsazepine / sensory perception of mechanical stimulus / peptide secretion / detection of chemical stimulus involved in sensory perception of pain / smooth muscle contraction involved in micturition / cellular response to acidic pH / fever generation / detection of temperature stimulus involved in thermoception / dendritic spine membrane / diet induced thermogenesis / behavioral response to pain / extracellular ligand-gated monoatomic ion channel activity / detection of temperature stimulus involved in sensory perception of pain / calcium ion import across plasma membrane / phosphoprotein binding / calcium channel activity / lipid metabolic process / 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
Chem-POV / 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoinositol / Transient receptor potential cation channel subfamily V member 1
Similarity search - Component
Biological speciesIctidomys tridecemlineatus (thirteen-lined ground squirrel)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.19 Å
AuthorsNadezhdin, K.D. / Neuberger, A. / Sobolevsky, A.I.
Funding support United States, 4items
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, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Assembly

Deposited unit
A: Osm-9-like TRP channel 1
B: Osm-9-like TRP channel 1
C: Osm-9-like TRP channel 1
D: Osm-9-like TRP channel 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)411,34042
Polymers383,6114
Non-polymers27,72938
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Osm-9-like TRP channel 1 / Transient receptor potential cation channel subfamily V member 1 / Vanilloid receptor 1


Mass: 95902.781 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ictidomys tridecemlineatus (thirteen-lined ground squirrel)
Gene: TRPV1 / Plasmid: pEG BacMam / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: I3LZN5
#2: Chemical...
ChemComp-POV / (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / POPC / POPC


Mass: 760.076 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: C42H82NO8P / Comment: phospholipid*YM
#3: Chemical
ChemComp-YBG / 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoinositol


Mass: 837.069 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C43H81O13P
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: sample 1 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightUnits: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Ictidomys tridecemlineatus (thirteen-lined ground squirrel)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMsodium chlorideNaClSodium chloride1
220 mMtris(hydroxymethyl)aminomethane1
30.01 %glyco-diosgenin (GDN)1
41 mMbeta-Mercaptoethanol2-Mercaptoethanol1
SpecimenConc.: 3.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: -2500 nm / Nominal defocus min: -800 nm / Cs: 2.7 mm
Image recordingAverage exposure time: 2.5 sec. / Electron dose: 65 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 11191
EM imaging opticsEnergyfilter slit width: 30 eV
Image scansWidth: 5760 / Height: 4092

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Processing

EM software
IDNameVersionCategory
1RELION3particle selection
2Leginonimage acquisition
4RELION3CTF correction
5Gctf1.06CTF correction
8Cootmodel fitting
10RELION3initial Euler assignment
11RELION3final Euler assignment
12RELION3classification
13RELION33D reconstruction
14PHENIXmodel refinement
CTF correctionType: NONE
Particle selectionNum. of particles selected: 6250182
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 3.19 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 54682 / Symmetry type: POINT
Atomic model buildingSpace: REAL

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