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- EMDB-66284: transient receptor potential V family member 3 -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-66284
Titletransient receptor potential V family member 3
Map data
Sample
  • Complex: transient receptor potential V family member 3
    • Protein or peptide: Isoform 2 of Transient receptor potential cation channel subfamily V member 3
  • Ligand: (5-fluoranylpyridin-2-yl)-[(3~{R})-3-[4-[4-fluoranyl-2-(trifluoromethyloxy)phenyl]-2-(hydroxymethyl)phenyl]pyrrolidin-1-yl]methanone
Keywordstransient receptor potential V family member 3 / ion channel / MEMBRANE PROTEIN
Function / homology
Function and homology information


negative regulation of hair cycle / osmosensory signaling pathway / response to temperature stimulus / positive regulation of calcium ion import / TRP channels / sodium channel activity / calcium ion import across plasma membrane / actin filament organization / calcium channel activity / calcium ion transmembrane transport ...negative regulation of hair cycle / osmosensory signaling pathway / response to temperature stimulus / positive regulation of calcium ion import / TRP channels / sodium channel activity / calcium ion import across plasma membrane / actin filament organization / calcium channel activity / calcium ion transmembrane transport / lysosome / cilium / signaling receptor complex / 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 repeat profile. / Ankyrin repeats (3 copies) / 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: 3.31 Å
AuthorsChen JH / Yu J
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: To Be Published
Title: Mechanism of Colivin Suppression of TRPV3 to Ameliorate Ulcerative Colitis.
Authors: Chen JH / Yu J
History
DepositionSep 19, 2025-
Header (metadata) releaseJul 15, 2026-
Map releaseJul 15, 2026-
UpdateJul 15, 2026-
Current statusJul 15, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66284.png

Downloads & links

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Map

FileDownload / File: emd_66284.map.gz / Format: CCP4 / Size: 125 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 320 pix.
= 337.6 Å		1.06 Å/pix.
x 320 pix.
= 337.6 Å		1.06 Å/pix.
x 320 pix.
= 337.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.055 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-1.2772162 - 2.365603
Average (Standard dev.)0.0011708152 (±0.047121566)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 337.59998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_66284_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_66284_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_66284_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : transient receptor potential V family member 3

EntireName: transient receptor potential V family member 3
Components
  • Complex: transient receptor potential V family member 3
    • Protein or peptide: Isoform 2 of Transient receptor potential cation channel subfamily V member 3
  • Ligand: (5-fluoranylpyridin-2-yl)-[(3~{R})-3-[4-[4-fluoranyl-2-(trifluoromethyloxy)phenyl]-2-(hydroxymethyl)phenyl]pyrrolidin-1-yl]methanone

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Supramolecule #1: transient receptor potential V family member 3

SupramoleculeName: transient receptor potential V family member 3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Isoform 2 of Transient receptor potential cation channel subfamil...

MacromoleculeName: Isoform 2 of 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: 90.813891 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKAHPKEMVP LMGKRVAAPS GNPAILPEKR PAEITPTKKS AHFFLEIEGF EPNPTVAKTS PPVFSKPMDS NIRQCISGNC DDMDSPQSP QDDVTETPSN PNSPSAQLAK EEQRRKKRRL KKRIFAAVSE GCVEELVELL VELQELCRRR HDEDVPDFLM H KLTASDTG ...String:
MKAHPKEMVP LMGKRVAAPS GNPAILPEKR PAEITPTKKS AHFFLEIEGF EPNPTVAKTS PPVFSKPMDS NIRQCISGNC DDMDSPQSP QDDVTETPSN PNSPSAQLAK EEQRRKKRRL KKRIFAAVSE GCVEELVELL VELQELCRRR HDEDVPDFLM H KLTASDTG KTCLMKALLN INPNTKEIVR ILLAFAEEND ILGRFINAEY TEEAYEGQTA LNIAIERRQG DIAALLIAAG AD VNAHAKG AFFNPKYQHE GFYFGETPLA LAACTNQPEI VQLLMEHEQT DITSRDSRGN NILHALVTVA EDFKTQNDFV KRM YDMILL RSGNWELETT RNNDGLTPLQ LAAKMGKAEI LKYILSREIK EKRLRSLSRK FTDWAYGPVS SSLYDLTNVD TTTD NSVLE ITVYNTNIDN RHEMLTLEPL HTLLHMKWKK FAKHMFFLSF CFYFFYNITL TLVSYYRPRE EEAIPHPLAL THKMG WLQL LGRMFVLIWA MCISVKEGIA IFLLRPSDLQ SILSDAWFHF VFFIQAVLVI LSVFLYLFAY KEYLACLVLA MALGWA NML YYTRGFQSMG MYSVMIQKVI LHDVLKFLFV YIVFLLGFGV ALASLIEKCP KDNKDCSSYG SFSDAVLELF KLTIGLG DL NIQQNSKYPI LFLFLLITYV ILTFVLLLNM LIALMGETVE NVSKESERIW RLQRARTILE FEKMLPEWLR SRFRMGEL C KVAEDDFRLC LRINEVKWTE WKTHVSFLNE DPGPVRRTAD FNKIQDSSRN NSKTTLNAFE EVEEFPETSV

UniProtKB: Transient receptor potential cation channel subfamily V member 3

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Macromolecule #2: (5-fluoranylpyridin-2-yl)-[(3~{R})-3-[4-[4-fluoranyl-2-(trifluoro...

MacromoleculeName: (5-fluoranylpyridin-2-yl)-[(3~{R})-3-[4-[4-fluoranyl-2-(trifluoromethyloxy)phenyl]-2-(hydroxymethyl)phenyl]pyrrolidin-1-yl]methanone
type: ligand / ID: 2 / Number of copies: 4 / Formula: A1EYQ
Molecular weightTheoretical: 478.411 Da

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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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm
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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.31 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 217509
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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