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- EMDB-20192: Structure of the TRPV3 K169A sensitized mutant in apo form at 4.1... -

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Basic information

Entry
Database: EMDB / ID: EMD-20192
TitleStructure of the TRPV3 K169A sensitized mutant in apo form at 4.1 A resolution
Map data
SampleHuman TRPV3 ion channel
  • Transient receptor potential cation channel subfamily V member 3
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsZubcevic L / Borschel WF / Hsu AL / Borgnia MJ / Lee S-Y
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 ReportPDB-ID: 6ot2

SummaryFull reportAbout validation report
History
DepositionMay 2, 2019-
Header (metadata) releaseMay 15, 2019-
Map releaseMay 22, 2019-
UpdateMay 22, 2019-
Current statusMay 22, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.017
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.017
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6ot2
  • Surface level: 0.017
  • Imaged by UCSF Chimera
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Structure viewerEM map:
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Supplemental images

Downloads & links

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Map

FileDownload / File: emd_20192.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 256 pix.
= 271.36 Å
1.06 Å/pix.
x 256 pix.
= 271.36 Å
1.06 Å/pix.
x 256 pix.
= 271.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density
Contour LevelBy AUTHOR: 0.017 / Movie #1: 0.017
Minimum - Maximum-0.039669726 - 0.064509355
Average (Standard dev.)0.000003817555 (±0.0027299428)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 271.36 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z271.360271.360271.360
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ513513513
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0400.0650.000

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Supplemental data

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Sample components

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Entire Human TRPV3 ion channel

EntireName: Human TRPV3 ion channel / Number of components: 2

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Component #1: protein, Human TRPV3 ion channel

ProteinName: Human TRPV3 ion channel / Recombinant expression: No
MassTheoretical: 320 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

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Component #2: protein, Transient receptor potential cation channel subfamily V ...

ProteinName: Transient receptor potential cation channel subfamily V member 3
Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 84.445477 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 2.5 mg/mL / pH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: OTHER / Accelerating voltage: 300 kV / Electron dose: 40 e/Å2 / Illumination mode: OTHER
LensImaging mode: OTHER
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C4 (4 fold cyclic) / Number of projections: 95184
3D reconstructionResolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF

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