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- EMDB-70595: Structure of wild-type human TRPC3 -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-70595
TitleStructure of wild-type human TRPC3
Map data
Sample
  • Complex: Wild-type human TRPC3 tetrameric complex
    • Protein or peptide: Short transient receptor potential channel 3
  • Ligand: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
KeywordsTRPC3 / cerebellar ataxia / moonwalker / MEMBRANE PROTEIN
Function / homology
Function and homology information


Role of second messengers in netrin-1 signaling / positive regulation of cardiac muscle hypertrophy in response to stress / store-operated calcium channel activity / Effects of PIP2 hydrolysis / Elevation of cytosolic Ca2+ levels / inositol 1,4,5 trisphosphate binding / cation channel complex / calcium-activated cation channel activity / TRP channels / response to ATP ...Role of second messengers in netrin-1 signaling / positive regulation of cardiac muscle hypertrophy in response to stress / store-operated calcium channel activity / Effects of PIP2 hydrolysis / Elevation of cytosolic Ca2+ levels / inositol 1,4,5 trisphosphate binding / cation channel complex / calcium-activated cation channel activity / TRP channels / response to ATP / positive regulation of calcium ion transport into cytosol / phototransduction / single fertilization / regulation of cytosolic calcium ion concentration / MECP2 regulates neuronal receptors and channels / response to calcium ion / calcium ion transmembrane transport / calcium channel activity / calcium ion transport / metal ion binding / plasma membrane
Similarity search - Function
Transient receptor potential channel, canonical 3 / Transient receptor ion channel domain / Transient receptor ion channel II / Transient receptor ion channel II / Transient receptor potential channel, canonical / Ankyrin repeats (3 copies) / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily ...Transient receptor potential channel, canonical 3 / Transient receptor ion channel domain / Transient receptor ion channel II / Transient receptor ion channel II / Transient receptor potential channel, canonical / 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
Short transient receptor potential channel 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsBell B / Baker ML / Cordero-Morales JF
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM149218 United States
CitationJournal: To Be Published
Title: Functional and Structural Basis of a Hypermorphic TRPC3 variant
Authors: Bell B / Jaramillo-Granada AM / Romero LO / Gutierrez IA / Mallampalli VKPS / Fan G / Varma S / Baker ML / Serysheva II / Vasquez V / Cordero-Morales JF
History
DepositionMay 12, 2025-
Header (metadata) releaseMar 25, 2026-
Map releaseMar 25, 2026-
UpdateMar 25, 2026-
Current statusMar 25, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70595.png

Downloads & links

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Map

FileDownload / File: emd_70595.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 300 pix.
= 324. Å		1.08 Å/pix.
x 300 pix.
= 324. Å		1.08 Å/pix.
x 300 pix.
= 324. 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: 0.185
Minimum - Maximum-1.3524987 - 2.1276596
Average (Standard dev.)-0.0012508164 (±0.04758369)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 324.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_70595_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_70595_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 : Wild-type human TRPC3 tetrameric complex

EntireName: Wild-type human TRPC3 tetrameric complex
Components
  • Complex: Wild-type human TRPC3 tetrameric complex
    • Protein or peptide: Short transient receptor potential channel 3
  • Ligand: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE

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Supramolecule #1: Wild-type human TRPC3 tetrameric complex

SupramoleculeName: Wild-type human TRPC3 tetrameric complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Short transient receptor potential channel 3

MacromoleculeName: Short transient receptor potential channel 3 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 97.465836 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEGSPSLRRM TVMREKGRRQ AVRGPAFMFN DRGTSLTAEE ERFLDAAEYG NIPVVRKMLE ESKTLNVNCV DYMGQNALQL AVGNEHLEV TELLLKKENL ARIGDALLLA ISKGYVRIVE AILNHPGFAA SKRLTLSPCE QELQDDDFYA YDEDGTRFSP D ITPIILAA ...String:
MEGSPSLRRM TVMREKGRRQ AVRGPAFMFN DRGTSLTAEE ERFLDAAEYG NIPVVRKMLE ESKTLNVNCV DYMGQNALQL AVGNEHLEV TELLLKKENL ARIGDALLLA ISKGYVRIVE AILNHPGFAA SKRLTLSPCE QELQDDDFYA YDEDGTRFSP D ITPIILAA HCQKYEVVHM LLMKGARIER PHDYFCKCGD CMEKQRHDSF SHSRSRINAY KGLASPAYLS LSSEDPVLTA LE LSNELAK LANIEKEFKN DYRKLSMQCK DFVVGVLDLC RDSEEVEAIL NGDLESAEPL EVHRHKASLS RVKLAIKYEV KKF VAHPNC QQQLLTIWYE NLSGLREQTI AIKCLVVLVV ALGLPFLAIG YWIAPCSRLG KILRSPFMKF VAHAASFIIF LGLL VFNAS DRFEGITTLP NITVTDYPKQ IFRVKTTQFT WTEMLIMVWV LGMMWSECKE LWLEGPREYI LQLWNVLDFG MLSIF IAAF TARFLAFLQA TKAQQYVDSY VQESDLSEVT LPPEIQYFTY ARDKWLPSDP QIISEGLYAI AVVLSFSRIA YILPAN ESF GPLQISLGRT VKDIFKFMVL FIMVFFAFMI GMFILYSYYL GAKVNAAFTT VEESFKTLFW SIFGLSEVTS VVLKYDH KF IENIGYVLYG IYNVTMVVVL LNMLIAMINS SYQEIEDDSD VEWKFARSKL WLSYFDDGKT LPPPFSLVPS PKSFVYFI M RIVNFPKCRR RRLQKDIEMG MGNSKSRLNL FTQSNSRVFE SHSFNSILNQ PTRYQQIMKR LIKRYVLKAQ VDKENDEVN EGELKEIKQD ISSLRYELLE DKSQATEELA ILIHKLSEKL NPSMLRCE

UniProtKB: Short transient receptor potential channel 3

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Macromolecule #2: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 2 / Number of copies: 12 / Formula: CPL
Molecular weightTheoretical: 758.06 Da
Chemical component information

ChemComp-CPL:
1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / phospholipid*YM

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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
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / 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 / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000
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: OTHER
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 127478
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7dxd


Chain - Source name: PDB / Chain - Initial model type: experimental model / Details: used for refinement into the map
Output model

PDB-9olk:
Structure of wild-type human TRPC3

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