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- PDB-9p6b: Cryo-EM structure of full-length human TRPV1 in the presence of a... -

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Basic information

Entry
Database: PDB / ID: 9p6b
TitleCryo-EM structure of full-length human TRPV1 in the presence of alpha-humulene
ComponentsTransient receptor potential cation channel subfamily V member 1
KeywordsMEMBRANE PROTEIN / transient receptor potential V family member 1 / TRP / channel / TRPV1 / TRP channels / sesquiterpene / alpha-humulene / pain / analgesia
Function / homology
Function and homology information


chemosensory behavior / response to capsazepine / sensory perception of mechanical stimulus / peptide secretion / excitatory extracellular ligand-gated monoatomic ion channel activity / temperature-gated ion channel activity / detection of chemical stimulus involved in sensory perception of pain / smooth muscle contraction involved in micturition / fever generation / thermoception ...chemosensory behavior / response to capsazepine / sensory perception of mechanical stimulus / peptide secretion / excitatory extracellular ligand-gated monoatomic ion channel activity / temperature-gated ion channel activity / detection of chemical stimulus involved in sensory perception of pain / smooth muscle contraction involved in micturition / fever generation / thermoception / detection of temperature stimulus involved in thermoception / cellular response to acidic pH / dendritic spine membrane / cellular response to ATP / TRP channels / cellular response to alkaloid / diet induced thermogenesis / detection of temperature stimulus involved in sensory perception of pain / intracellularly gated calcium channel activity / behavioral response to pain / calcium ion import across plasma membrane / voltage-gated calcium channel activity / extracellular ligand-gated monoatomic ion channel activity / phosphatidylinositol binding / phosphoprotein binding / GABA-ergic synapse / calcium ion transmembrane transport / calcium channel activity / lipid metabolic process / transmembrane signaling receptor activity / sensory perception of taste / cellular response to heat / protein homotetramerization / postsynaptic membrane / cell surface receptor signaling pathway / calmodulin binding / negative regulation of transcription by RNA polymerase II / ATP binding / metal ion 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
Chem-8IJ / Chem-POV / TRIDECANE / Transient receptor potential cation channel subfamily V member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.74 Å
AuthorsTalyzina, I.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 Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)R01 AR078814 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01 NS107253 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R37 NS083660 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2025
Title: Structural basis of the inhibition of TRPV1 by analgesic sesquiterpenes
Authors: Sanchez-Hernandez, R. / Benitez-Angeles, M. / Talyzina, I.A. / Llorente, I. / Gonzalez-Avendano, M. / Sierra, F. / Mendez-Resendiz, A. / Mercado, F. / Vergara-Jaque, A. / Sobolevsky, A.I. / ...Authors: Sanchez-Hernandez, R. / Benitez-Angeles, M. / Talyzina, I.A. / Llorente, I. / Gonzalez-Avendano, M. / Sierra, F. / Mendez-Resendiz, A. / Mercado, F. / Vergara-Jaque, A. / Sobolevsky, A.I. / Islas, L.D. / Rosenbaum, T.
History
DepositionJun 18, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transient receptor potential cation channel subfamily V member 1
B: Transient receptor potential cation channel subfamily V member 1
C: Transient receptor potential cation channel subfamily V member 1
D: Transient receptor potential cation channel subfamily V member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)526,87646
Polymers498,3014
Non-polymers28,57442
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Transient receptor potential cation channel subfamily V member 1 / TrpV1 / Capsaicin receptor / Osm-9-like TRP channel 1 / OTRPC1 / Vanilloid receptor 1


Mass: 124575.281 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRPV1, VR1 / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: Q8NER1

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Non-polymers , 5 types, 134 molecules

#2: Chemical...
ChemComp-POV / (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / POPC


Mass: 760.076 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: C42H82NO8P / Comment: phospholipid*YM
#3: Chemical
ChemComp-8IJ / (2R)-3-{[(R)-hydroxy{[(1S,2R,3R,4S,5S,6R)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dioctadecanoate


Mass: 867.138 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C45H87O13P
#4: Chemical
ChemComp-TRD / TRIDECANE / LIPID FRAGMENT


Mass: 184.361 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C13H28
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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: full-length human TRPV1 in the presence of alpha-humulene
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.50 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Cell: Human embryonic kidney 293 / Plasmid: pEG BacMam
Buffer solutionpH: 7
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMsodium chlorideNaCl1
250 mM(4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid)HEPES1
31 mMbeta-MercaptoethanolbME1
SpecimenConc.: 2.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: human TRPV1
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 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 FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 700 nm / Cs: 2.7 mm
Image recordingAverage exposure time: 1.318 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 9208
Image scansWidth: 5760 / Height: 4092

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Processing

EM software
IDNameVersionCategory
1cryoSPARCv4.4particle selection
4cryoSPARCv4.4CTF correction
9cryoSPARCv4.4initial Euler assignment
10cryoSPARCv4.4final Euler assignment
11cryoSPARCv4.4classification
12cryoSPARCv4.43D reconstruction
13PHENIX1.11.1_2575model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1693063
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 2.74 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 226949 / Symmetry type: POINT
Atomic model buildingSpace: REAL
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00644136
ELECTRON MICROSCOPYf_angle_d0.94978456
ELECTRON MICROSCOPYf_dihedral_angle_d12.41318664
ELECTRON MICROSCOPYf_chiral_restr0.0523316
ELECTRON MICROSCOPYf_plane_restr0.0046468

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