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- PDB-9dij: 4 Angstrom structure of the human TRPV3 pentamer -

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Basic information

Entry
Database: PDB / ID: 9dij
Title4 Angstrom structure of the human TRPV3 pentamer
ComponentsTransient receptor potential cation channel subfamily V member 3
KeywordsMEMBRANE PROTEIN / Ion channel / transient receptor potential channel / alternative oligomeric state / pore dilation
Function / homology
Function and homology information


negative regulation of hair cycle / osmosensory signaling pathway / TRP channels / response to temperature stimulus / sodium channel activity / positive regulation of calcium ion import / calcium ion import across plasma membrane / actin filament organization / calcium ion transmembrane transport / calcium channel activity ...negative regulation of hair cycle / osmosensory signaling pathway / TRP channels / response to temperature stimulus / sodium channel activity / positive regulation of calcium ion import / calcium ion import across plasma membrane / actin filament organization / calcium ion transmembrane transport / calcium channel activity / lysosome / receptor complex / cilium / metal ion binding / identical protein binding / plasma membrane / cytoplasm
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 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.07 Å
AuthorsLansky, S. / Clarke, O.B. / Scheuring, S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS134559 United States
National Institutes of Health/National Center for Complementary and Integrative Health (NIH/NCCIH)DP1AT010874 United States
CitationJournal: Nat Commun / Year: 2025
Title: Structural dynamics and permeability of the TRPV3 pentamer.
Authors: Shifra Lansky / Zhaokun Wang / Oliver B Clarke / Christophe Chipot / Simon Scheuring /
Abstract: TRPV3 belongs to the large superfamily of tetrameric transient receptor potential (TRP) ion channels. Recently, using high-speed atomic force microscopy (HS-AFM), we discovered a rare and transient ...TRPV3 belongs to the large superfamily of tetrameric transient receptor potential (TRP) ion channels. Recently, using high-speed atomic force microscopy (HS-AFM), we discovered a rare and transient pentameric state for TRPV3 that is in equilibrium with the tetrameric state, and, using cryo-EM, we solved a low-resolution structure of the TRPV3 pentamer, in which, however, many residues were unresolved. Here, we present a higher resolution and more complete structure of the pentamer, revealing a domain-swapped architecture, a collapsed vanilloid binding site, and a large pore. Molecular dynamics simulations and potential of mean force calculations of the pentamer establish high protein dynamics and permeability to large cations. Subunit interface analysis, together with thermal denaturation experiments, led us to propose a molecular mechanism of the tetramer-to-pentamer transition, backed experimentally by HS-AFM observations. Collectively, our data demonstrate that the TRPV3 pentamer is in a hyper-activated state with unique, highly permissive permeation properties.
History
DepositionSep 5, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 21, 2025Provider: repository / Type: Initial release
Revision 1.1May 28, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
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 / _citation_author.identifier_ORCID / _em_admin.last_update

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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 3
B: Transient receptor potential cation channel subfamily V member 3
C: Transient receptor potential cation channel subfamily V member 3
D: Transient receptor potential cation channel subfamily V member 3
E: Transient receptor potential cation channel subfamily V member 3


Theoretical massNumber of molelcules
Total (without water)463,3455
Polymers463,3455
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, high-speed atomic force microscopy was used to discover this oligomeric state. The pentameric state is a rare state.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Transient receptor potential cation channel subfamily V member 3 / TrpV3 / Vanilloid receptor-like 3 / VRL-3


Mass: 92669.000 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRPV3 / Cell line (production host): HEK293S GnTI- / Production host: Homo sapiens (human) / References: UniProt: Q8NET8
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: TRPV3 ion channel / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMtris(hydroxymethyl)aminomethaneTris1
2150 mMsodium chlorideNaCl1
30.01 %glyco diosgeninGDN1
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 64000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm / Cs: 0.001 mm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 53.27 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 10118

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2Leginonimage acquisition
4cryoSPARCCTF correction
8PHENIXmodel refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3668517
SymmetryPoint symmetry: C5 (5 fold cyclic)
3D reconstructionResolution: 4.07 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 51588 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00225125
ELECTRON MICROSCOPYf_angle_d0.46833995
ELECTRON MICROSCOPYf_dihedral_angle_d3.1863275
ELECTRON MICROSCOPYf_chiral_restr0.0353885
ELECTRON MICROSCOPYf_plane_restr0.0024235

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