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- PDB-13ll: Structure of human TRPV3-Q580P Olmsted syndrome mutant in the clo... -

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Basic information

Entry
Database: PDB / ID: 13ll
TitleStructure of human TRPV3-Q580P Olmsted syndrome mutant in the closed state
ComponentsIsoform 2 of Transient receptor potential cation channel subfamily V member 3,Green fluorescent protein
KeywordsMEMBRANE PROTEIN / TRPV3 / Olmsted syndrome / Q580P / closed state / mutation / gain-of-function
Function / homology
Function and homology information


negative regulation of hair cycle / osmosensory signaling pathway / response to temperature stimulus / TRP channels / positive regulation of calcium ion import / sodium channel activity / calcium ion import across plasma membrane / bioluminescence / actin filament organization / generation of precursor metabolites and energy ...negative regulation of hair cycle / osmosensory signaling pathway / response to temperature stimulus / TRP channels / positive regulation of calcium ion import / sodium channel activity / calcium ion import across plasma membrane / bioluminescence / actin filament organization / generation of precursor metabolites and energy / calcium ion transmembrane transport / calcium channel activity / lysosome / signaling 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 / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Ankyrin repeat profile. / Ankyrin repeats (3 copies) / Ankyrin repeat region circular profile. ...Transient receptor potential cation channel subfamily V member 1-4 / Transient receptor potential cation channel subfamily V / Ankyrin repeat / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Ankyrin repeat profile. / Ankyrin repeats (3 copies) / 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 / Green fluorescent protein / Transient receptor potential cation channel subfamily V member 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Aequorea victoria (jellyfish)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.96 Å
AuthorsKhau, J. / Nadezhdin, K.D. / Purohit, R. / Sobolevsky, A.I.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)R01 AR078814 United States
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
CitationJournal: Nat Commun / Year: 2026
Title: Structural diversity of heat-sensing channel TRPV3 with Olmsted syndrome mutations.
Authors: Jeffrey Khau / Rutambhara Purohit / Kirill D Nadezhdin / Irina A Talyzina / Alexander I Sobolevsky /
Abstract: Mutations in TRPV3, a temperature-sensitive ion channel critical for skin physiology, cause severe genodermatosis called Olmsted syndrome (OS). Here we integrate single-channel recordings and cryo-EM ...Mutations in TRPV3, a temperature-sensitive ion channel critical for skin physiology, cause severe genodermatosis called Olmsted syndrome (OS). Here we integrate single-channel recordings and cryo-EM to characterize five OS mutants. All exhibit reduced temperature sensitivity in the temperature range relevant to normal skin physiology and disrupt structural elements stabilizing non-conducting states, including vanilloid lipid coordination and S4-S5 linker-TRP helix contacts. Despite shared gain-of-function phenotype, the mutations cause different distributions of the TRPV3 closed, open, and inactivated states. One mutation expands the conformational ensemble with noncanonical two-fold-symmetrical states featuring dramatic domain swapping. Our findings highlight conserved TRP channel gating mechanisms and suggest that OS mutations alter TRPV3 function by triggering the conformational wave that mediates gating in wild-type channels. These insights establish a framework to decode genotype-structure-function relationships in TRP channelopathies and guide future therapeutic strategies.
History
DepositionMay 13, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform 2 of Transient receptor potential cation channel subfamily V member 3,Green fluorescent protein
B: Isoform 2 of Transient receptor potential cation channel subfamily V member 3,Green fluorescent protein
C: Isoform 2 of Transient receptor potential cation channel subfamily V member 3,Green fluorescent protein
D: Isoform 2 of Transient receptor potential cation channel subfamily V member 3,Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)507,86043
Polymers480,4284
Non-polymers27,43239
Water2,252125
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Isoform 2 of Transient receptor potential cation channel subfamily V member 3,Green fluorescent protein


Mass: 120106.961 Da / Num. of mol.: 4 / Mutation: Q580P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Aequorea victoria (jellyfish)
Gene: TRPV3, GFP / Production host: Homo sapiens (human) / References: UniProt: Q8NET8, UniProt: P42212
#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.: 36 / Source method: obtained synthetically / Formula: C42H82NO8P / Comment: phospholipid*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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 tetramer / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
31Aequorea victoria (jellyfish)6100
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMsodium chlorideNaCl1
220 mMTris-HCl1
30.01 %glyco-diosgenin (GDN)1
41 mMbeta-mercaptoethanol1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: 1500 nm / Nominal defocus min: 500 nm
Image recordingAverage exposure time: 2.3 sec. / Electron dose: 60.8 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 23376

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
12cryoSPARC3D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 119430 / Symmetry type: POINT
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0143364
ELECTRON MICROSCOPYf_angle_d0.94677236
ELECTRON MICROSCOPYf_dihedral_angle_d14.63818256
ELECTRON MICROSCOPYf_chiral_restr0.0563244
ELECTRON MICROSCOPYf_plane_restr0.0056320

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