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- PDB-6ot5: Structure of the TRPV3 K169A sensitized mutant in the presence of... -

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Basic information

Entry
Database: PDB / ID: 6ot5
TitleStructure of the TRPV3 K169A sensitized mutant in the presence of 2-APB at 3.6 A resolution
ComponentsTransient receptor potential cation channel subfamily V member 3,Transient receptor potential cation channel subfamily V member 3
KeywordsTRANSPORT PROTEIN / Ion channel / TRP channel / TRPV channel / Metal transport / Membrane transport / membrane protein
Function / homology
Function and homology information


TRP channels / negative regulation of hair cycle / positive regulation of calcium ion import / calcium channel activity / calcium ion transmembrane transport / ion channel activity / response to heat / receptor complex / integral component of plasma membrane / plasma membrane
Transient receptor potential channel, vanilloid 1-4 / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Transient receptor potential channel, vanilloid 3 / Transient receptor potential cation channel subfamily V / Ankyrin repeat-containing domain / Ion transport domain / Ankyrin repeat / Ion transport protein / Ankyrin repeats (3 copies) ...Transient receptor potential channel, vanilloid 1-4 / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Transient receptor potential channel, vanilloid 3 / Transient receptor potential cation channel subfamily V / Ankyrin repeat-containing domain / Ion transport domain / Ankyrin repeat / Ion transport protein / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile.
Transient receptor potential cation channel subfamily V member 3
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsZubcevic, L. / Borschel, W.F. / Hsu, A.L. / Borgnia, M.J. / Lee, S.-Y.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and StrokeR35NS097241 United States
National Institutes of Health/National Institute of Environmental Health SciencesZIC ES103326 United States
CitationJournal: Elife / Year: 2019
Title: Regulatory switch at the cytoplasmic interface controls TRPV channel gating.
Authors: Lejla Zubcevic / William F Borschel / Allen L Hsu / Mario J Borgnia / Seok-Yong Lee /
Abstract: Temperature-sensitive transient receptor potential vanilloid (thermoTRPV) channels are activated by ligands and heat, and are involved in various physiological processes. ThermoTRPV channels possess ...Temperature-sensitive transient receptor potential vanilloid (thermoTRPV) channels are activated by ligands and heat, and are involved in various physiological processes. ThermoTRPV channels possess a large cytoplasmic ring consisting of N-terminal ankyrin repeat domains (ARD) and C-terminal domains (CTD). The cytoplasmic inter-protomer interface is unique and consists of a CTD coiled around a β-sheet which makes contacts with the neighboring ARD. Despite much existing evidence that the cytoplasmic ring is important for thermoTRPV function, the mechanism by which this unique structure is involved in thermoTRPV gating has not been clear. Here, we present cryo-EM and electrophysiological studies which demonstrate that TRPV3 gating involves large rearrangements at the cytoplasmic inter-protomer interface and that this motion triggers coupling between cytoplasmic and transmembrane domains, priming the channel for opening. Furthermore, our studies unveil the role of this interface in the distinct biophysical and physiological properties of individual thermoTRPV subtypes.
Validation Report
SummaryFull reportAbout validation report
History
DepositionMay 2, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2019Provider: repository / Type: Initial release

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Assembly

Deposited unit
A: Transient receptor potential cation channel subfamily V member 3,Transient receptor potential cation channel subfamily V member 3
B: Transient receptor potential cation channel subfamily V member 3,Transient receptor potential cation channel subfamily V member 3
C: Transient receptor potential cation channel subfamily V member 3,Transient receptor potential cation channel subfamily V member 3
D: Transient receptor potential cation channel subfamily V member 3,Transient receptor potential cation channel subfamily V member 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)332,8288
Polymers331,9274
Non-polymers9004
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area21140 Å2
ΔGint-200 kcal/mol
Surface area117020 Å2

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Components

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


Mass: 82981.859 Da / Num. of mol.: 4 / Mutation: T96A, K169A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRPV3 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8NET8
#2: Chemical
ChemComp-FZ4 / 2-aminoethyl diphenylborinate


Mass: 225.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H16BNO

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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: Human TRPV3 ion channel / Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
Molecular weightValue: 0.32 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 8
SpecimenConc.: 2.5 mg/ml / Details: Monodisperse sample / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: OTHER / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER
Image recordingElectron dose: 42 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.12_2829: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 79006 / Num. of class averages: 1 / Symmetry type: POINT
Refine LS restraints

Refinement-ID: ELECTRON MICROSCOPY

TypeDev idealNumber
f_bond_d0.00734176
f_angle_d0.83561268
f_dihedral_angle_d8.11913860
f_chiral_restr0.0463016
f_plane_restr0.0045504

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