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- EMDB-20194: Structure of the TRPV3 K169A sensitized mutant in the presence of... -

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Basic information

Entry
Database: EMDB / ID: EMD-20194
TitleStructure of the TRPV3 K169A sensitized mutant in the presence of 2-APB at 3.6 A resolution
Map dataFull map
Sample
  • Complex: Human TRPV3 ion channel
    • Protein or peptide: Transient receptor potential cation channel subfamily V member 3,Transient receptor potential cation channel subfamily V member 3
  • Ligand: 2-aminoethyl diphenylborinate
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: 3.6 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 22, 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: 0.04
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.04
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  • Surface view with fitted model
  • Atomic models: PDB-6ot5
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20194.png

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Map

FileDownload / File: emd_20194.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.)
1.08 Å/pix.
x 256 pix.
= 276.48 Å		1.08 Å/pix.
x 256 pix.
= 276.48 Å		1.08 Å/pix.
x 256 pix.
= 276.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.04
Minimum - Maximum-0.15243746 - 0.26606923
Average (Standard dev.)0.000009427482 (±0.008201666)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 276.48 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.081.081.08
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z276.480276.480276.480
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-0.1520.2660.000

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Supplemental data

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Half map: Half map 1

Fileemd_20194_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_20194_half_map_2.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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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,Transient receptor potential cation channel subfamily V member 3
  • Ligand: 2-aminoethyl diphenylborinate

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Supramolecule #1: Human TRPV3 ion channel

SupramoleculeName: Human TRPV3 ion channel / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
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,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: 82.981859 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)EEQRRKKR RLKKRIFAAV SE GCVEELV ELLVELQELC RRRHDEDVPD FLMHKLTASD TGATCLMKAL LNINPNTKEI VRILLAFAEE NDILGRFINA EYT EEAYEG QTALNIAIER ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)EEQRRKKR RLKKRIFAAV SE GCVEELV ELLVELQELC RRRHDEDVPD FLMHKLTASD TGATCLMKAL LNINPNTKEI VRILLAFAEE NDILGRFINA EYT EEAYEG QTALNIAIER RQGDIAALLI AAGADVNAHA KGAFFNPKYQ HEGFYFGETP LALAACTNQP EIVQLLMEHE QTDI TSRDS RGNNILHALV TVAEDFKTQN DFVKRMYDMI LLRSGNWELE TTRNNDGLTP LQLAAKMGKA EILKYILSRE IKEKR LRSL SRKFTDWAYG PVSSSLYDLT NVDTTTDNSV LEITVYNTNI DNRHEMLTLE PLHTLLHMKW KKFAKHMFFL SFCFYF FYN ITLTLVSYYR PREEEAIPHP LALTHKMGWL QLLGRMFVLI WAMCISVKEG IAIFLLRPSD LQSILSDAWF HFVFFIQ AV LVILSVFLYL FAYKEYLACL VLAMALGWAN MLYYTRGFQS MGMYSVMIQK VILHDVLKFL FVYIVFLLGF GVALASLI E KCPKDNKDCS SYGSFSDAVL ELFKLTIGLG DLNIQQNSKY PILFLFLLIT YVILTFVLLL NMLIALMGET VENVSKESE RIWRLQRART ILEFEKMLPE WLRSRFRMGE LCKVAEDDFR LCLRINEVKW TEWKTHVSFL NEDPGPVRRT DFNKIQDSSR NNSKTTLNA FEEVEEFPET SVVDAGLEVL FQGDYKDDDD KAHHHHHH

UniProtKB: Transient receptor potential cation channel subfamily V member 3

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Macromolecule #2: 2-aminoethyl diphenylborinate

MacromoleculeName: 2-aminoethyl diphenylborinate / type: ligand / ID: 2 / Number of copies: 4 / Formula: FZ4
Molecular weightTheoretical: 225.094 Da
Chemical component information

ChemComp-FZ4:
2-aminoethyl diphenylborinate

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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
GridPretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Details: unspecified
VitrificationCryogen name: ETHANE
DetailsMonodisperse sample

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 42.0 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: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 79006
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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