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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 dataFull map
Sample
  • Complex: Human TRPV3 ion channel
    • Protein or peptide: Transient receptor potential cation channel subfamily V member 3
KeywordsIon channel / TRP channel / TRPV channel / Metal transport / Membrane transport / membrane protein / TRANSPORT PROTEIN
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 / actin filament organization / calcium ion transmembrane transport / calcium channel activity ...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 / actin filament organization / calcium ion transmembrane transport / calcium channel activity / lysosome / 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 / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Transient receptor potential cation channel subfamily V member 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsZubcevic L / Borschel WF
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R35NS097241 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)ZIC 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.
History
DepositionMay 2, 2019-
Header (metadata) releaseMay 15, 2019-
Map releaseMay 22, 2019-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing 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
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  • 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:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20192.png

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)
AnnotationFull map
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

Histogram

Histogram (log scale)
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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Half map: Half map 2

Fileemd_20192_half_map_1.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_20192_half_map_2.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human TRPV3 ion channel

EntireName: Human TRPV3 ion channel
Components
  • Complex: Human TRPV3 ion channel
    • Protein or peptide: Transient receptor potential cation channel subfamily V member 3

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Supramolecule #1: Human TRPV3 ion channel

SupramoleculeName: Human TRPV3 ion channel / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 320 KDa

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Macromolecule #1: Transient receptor potential cation channel subfamily V member 3

MacromoleculeName: Transient receptor potential cation channel subfamily V member 3
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 84.445477 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)PSNPNS PSAQ LAKEE QRRKKRRLKK RIFAAVSEGC VEELVELLVE LQELCRRRHD EDVPDFLMHK LTASDTGATC LMKALLNINP NTKEI VRIL LAFAEENDIL ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)PSNPNS PSAQ LAKEE QRRKKRRLKK RIFAAVSEGC VEELVELLVE LQELCRRRHD EDVPDFLMHK LTASDTGATC LMKALLNINP NTKEI VRIL LAFAEENDIL GRFINAEYTE EAYEGQTALN IAIERRQGDI AALLIAAGAD VNAHAKGAFF NPKYQHEGFY FGETPL ALA ACTNQPEIVQ LLMEHEQTDI TSRDSRGNNI LHALVTVAED FKTQNDFVKR MYDMILLRSG NWELETTRNN DGLTPLQ LA AKMGKAEILK YILSREIKEK RLRSLSRKFT DWAYGPVSSS LYDLTNVDTT TDNSVLEITV YNTNIDNRHE MLTLEPLH T LLHMKWKKFA KHMFFLSFCF YFFYNITLTL VSYYRPREEE AIPHPLALTH KMGWLQLLGR MFVLIWAMCI SVKEGIAIF LLRPSDLQSI LSDAWFHFVF FIQAVLVILS VFLYLFAYKE YLACLVLAMA LGWANMLYYT RGFQSMGMYS VMIQKVILHD VLKFLFVYI VFLLGFGVAL ASLIEKCPKD NKDCSSYGSF SDAVLELFKL TIGLGDLNIQ QNSKYPILFL FLLITYVILT F VLLLNMLI ALMGETVENV SKESERIWRL QRARTILEFE KMLPEWLRSR FRMGELCKVA EDDFRLCLRI NEVKWTEWKT HV SFLNEDP GPVRRTDFNK IQDSSRNNSK TTLNAFEEVE EFPETSVVDA GLEVLFQGDY KDDDDKAHHH HHH

UniProtKB: Transient receptor potential cation channel subfamily V member 3

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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

Concentration2.5 mg/mL
BufferpH: 8
GridModel: Quantifoil, UltrAuFoil, R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE
DetailsMonodisperse sample

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: OTHER
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

9115

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 95184
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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