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- PDB-6mhs: Structure of the human TRPV3 channel in a putative sensitized con... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6mhs | ||||||||||||
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Title | Structure of the human TRPV3 channel in a putative sensitized conformation | ||||||||||||
![]() | Transient receptor potential cation channel subfamily V member 3 | ||||||||||||
![]() | TRANSPORT PROTEIN / membrane protein / ion channel / TRP channel / calcium transport | ||||||||||||
Function / homology | ![]() negative regulation of hair cycle / TRP channels / response to temperature stimulus / positive regulation of calcium ion import / calcium ion transmembrane transport / calcium channel activity / receptor complex / lysosome / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||||||||
![]() | Zubcevic, L. / Herzik, M.A. / Wu, M. / Borschel, W.F. / Hirschi, M. / Song, A. / Lander, G.C. / Lee, S.Y. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Conformational ensemble of the human TRPV3 ion channel. Authors: Lejla Zubcevic / Mark A Herzik / Mengyu Wu / William F Borschel / Marscha Hirschi / Albert S Song / Gabriel C Lander / Seok-Yong Lee / ![]() Abstract: Transient receptor potential vanilloid channel 3 (TRPV3), a member of the thermosensitive TRP (thermoTRPV) channels, is activated by warm temperatures and serves as a key regulator of normal skin ...Transient receptor potential vanilloid channel 3 (TRPV3), a member of the thermosensitive TRP (thermoTRPV) channels, is activated by warm temperatures and serves as a key regulator of normal skin physiology through the release of pro-inflammatory messengers. Mutations in trpv3 have been identified as the cause of the congenital skin disorder, Olmsted syndrome. Unlike other members of the thermoTRPV channel family, TRPV3 sensitizes upon repeated stimulation, yet a lack of structural information about the channel precludes a molecular-level understanding of TRPV3 sensitization and gating. Here, we present the cryo-electron microscopy structures of apo and sensitized human TRPV3, as well as several structures of TRPV3 in the presence of the common thermoTRPV agonist 2-aminoethoxydiphenyl borate (2-APB). Our results show α-to-π-helix transitions in the S6 during sensitization, and suggest a critical role for the S4-S5 linker π-helix during ligand-dependent gating. | ||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 412.9 KB | Display | ![]() |
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PDB format | ![]() | 324.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 9117MC ![]() 9115C ![]() 9119C ![]() 9120C ![]() 9121C ![]() 6mhoC ![]() 6mhvC ![]() 6mhwC ![]() 6mhxC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 94860.219 Da / Num. of mol.: 4 / Mutation: T96A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Human TRPV3 in a putative sensitized state / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 8 |
Specimen | Conc.: 0.35 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: Gatan Solarus / Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil, UltrAuFoil, R1.2/1.3 |
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 277 K Details: Sample was manually blotted for 4 seconds prior to plunge-freezing into liquid ethane cooled by liquid nitrogen. |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA Details: Alignment performed as described in Herzik, Wu, Lander, Nat Methods 2017 (PMID: 28991891) |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 45000 X / Nominal defocus max: 1400 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 93 K / Temperature (min): 93 K |
Image recording | Average exposure time: 12 sec. / Electron dose: 67 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2982 |
Image scans | Sampling size: 5 µm / Width: 3710 / Height: 3838 / Movie frames/image: 47 / Used frames/image: 1-47 |
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Processing
Software | Name: PHENIX / Version: 1.10.1_2155: / Classification: refinement | ||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 559206 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C4 (4 fold cyclic) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 44554 / Algorithm: BACK PROJECTION / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 51 / Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Correlation coefficient | ||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 5AN8 Pdb chain-ID: A / Accession code: 5AN8 / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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