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- EMDB-8925: Cryo-EM structure of mouse TRPV3-Y564A -

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Basic information

Entry
Database: EMDB / ID: EMD-8925
TitleCryo-EM structure of mouse TRPV3-Y564A
Map dataprimary map
Sample
  • Complex: TRPV3
    • Protein or peptide: TRPV3-Y564A
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.5 Å
AuthorsSingh AK / McGoldrick LL / Sobolevsky AI
CitationJournal: Nat Struct Mol Biol / Year: 2018
Title: Structure and gating mechanism of the transient receptor potential channel TRPV3.
Authors: Appu K Singh / Luke L McGoldrick / Alexander I Sobolevsky /
Abstract: Transient receptor potential vanilloid subfamily member 3 (TRPV3) channel plays a crucial role in skin physiology and pathophysiology. Mutations in TRPV3 are associated with various skin diseases, ...Transient receptor potential vanilloid subfamily member 3 (TRPV3) channel plays a crucial role in skin physiology and pathophysiology. Mutations in TRPV3 are associated with various skin diseases, including Olmsted syndrome, atopic dermatitis, and rosacea. Here we present the cryo-electron microscopy structures of full-length mouse TRPV3 in the closed apo and agonist-bound open states. The agonist binds three allosteric sites distal to the pore. Channel opening is accompanied by conformational changes in both the outer pore and the intracellular gate. The gate is formed by the pore-lining S6 helices that undergo local α-to-π helical transitions, elongate, rotate, and splay apart in the open state. In the closed state, the shorter S6 segments are entirely α-helical, expose their nonpolar surfaces to the pore, and hydrophobically seal the ion permeation pathway. These findings further illuminate TRP channel activation and can aid in the design of drugs for the treatment of inflammatory skin conditions, itch, and pain.
History
DepositionJun 26, 2018-
Header (metadata) releaseJul 18, 2018-
Map releaseSep 5, 2018-
UpdateSep 19, 2018-
Current statusSep 19, 2018Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0268
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0268
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8925.png

Downloads & links

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Map

FileDownload / File: emd_8925.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationprimary map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.98 Å/pix.
x 200 pix.
= 196. Å		0.98 Å/pix.
x 200 pix.
= 196. Å		0.98 Å/pix.
x 200 pix.
= 196. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.98 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0268 / Movie #1: 0.0268
Minimum - Maximum-0.05922246 - 0.1026311
Average (Standard dev.)0.002545281 (±0.007573362)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 196.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.980.980.98
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z196.000196.000196.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.0590.1030.003

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Supplemental data

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Sample components

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Entire : TRPV3

EntireName: TRPV3
Components
  • Complex: TRPV3
    • Protein or peptide: TRPV3-Y564A

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Supramolecule #1: TRPV3

SupramoleculeName: TRPV3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Homo sapiens (human)

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Macromolecule #1: TRPV3-Y564A

MacromoleculeName: TRPV3-Y564A / type: protein_or_peptide / ID: 1 / Enantiomer: DEXTRO
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: mgahskemap lmgkrttapg gnpvvltekr padltptkks ahffleiegf epnptvtkts ppifskpmds nirqclsgnc ddmdspqspq ddvtetpsnp nspsanlake eqrqkkkrlk krifaavseg cveelrellq dlqdlcrrrr gldvpdflmh kltasdtgkt ...String:
mgahskemap lmgkrttapg gnpvvltekr padltptkks ahffleiegf epnptvtkts ppifskpmds nirqclsgnc ddmdspqspq ddvtetpsnp nspsanlake eqrqkkkrlk krifaavseg cveelrellq dlqdlcrrrr gldvpdflmh kltasdtgkt clmkallnin pntkeivril lafaeendil drfinaeyte eayegqtaln iaierrqgdi tavliaagad vnahakgvff npkyqhegfy fgetplalaa ctnqpeivql lmeneqtdit sqdsrgnnil halvtvaedf ktqndfvkrm ydmillrsgn weletmrnnd gltplqlaak mgkaeilkyi lsreikekpl rslsrkftdw aygpvsssly dltnvdtttd nsvleiivyn tnidnrheml tleplhtllh tkwkkfakym fflsfcfyff ynitltlvsy yrprededlp hplalthkms wlqllgrmfv liwatcisvk egiaifllrp sdlqsilsda wfhfvffvqa vlvilsvfly lfaykeylac lvlamalgwa nmlaytrgfq smgmysvmiq kvilhdvlkf lfvyilfllg fgvalaslie kcskdkkdcs sygsfsdavl elfkltiglg dlniqqnsty pilflfllit yviltfvlll nmlialmget venvskeser iwrlqrarti lefekmlpew lrsrfrmgel ckvadedfrl clrinevkwt ewkthvsfln edpgpirrta dlnkiqdssr snskttlyaf deldefpets v

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration4.0 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
20.0 mMTRISTRIS
0.08 mMGDNGDN
GridMaterial: GOLD / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy

MicroscopeFEI TECNAI F30
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 67.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

8919

Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 44661
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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