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- EMDB-62343: Cryo-EM structure of heteromeric TRPC channel -

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Basic information

Entry
Database: EMDB / ID: EMD-62343
TitleCryo-EM structure of heteromeric TRPC channel
Map data
Sample
  • Complex: Cryo-EM structure of heteromeric TRPC channel
    • Protein or peptide: Short transient receptor potential channel 1
    • Protein or peptide: Short transient receptor potential channel 5
  • Ligand: CALCIUM ION
  • Ligand: (2S)-2-(hexadecanoyloxy)-3-hydroxypropyl (9Z)-octadec-9-enoate
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: ZINC ION
KeywordsTRP / MEMBRANE PROTEIN
Function / homology
Function and homology information


regulation of membrane hyperpolarization / phosphatidylserine exposure on apoptotic cell surface / negative regulation of dendrite morphogenesis / Role of second messengers in netrin-1 signaling / store-operated calcium channel activity / melanin biosynthetic process / inositol 1,4,5 trisphosphate binding / cation channel complex / actinin binding / clathrin binding ...regulation of membrane hyperpolarization / phosphatidylserine exposure on apoptotic cell surface / negative regulation of dendrite morphogenesis / Role of second messengers in netrin-1 signaling / store-operated calcium channel activity / melanin biosynthetic process / inositol 1,4,5 trisphosphate binding / cation channel complex / actinin binding / clathrin binding / TRP channels / regulation of cardiac conduction / regulation of cytosolic calcium ion concentration / positive regulation of axon extension / monoatomic cation channel activity / Ion homeostasis / calcium channel complex / positive regulation of neuron differentiation / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / positive regulation of release of sequestered calcium ion into cytosol / response to calcium ion / calcium ion transmembrane transport / calcium channel activity / neuron differentiation / calcium ion transport / nervous system development / presynapse / positive regulation of cytosolic calcium ion concentration / actin binding / growth cone / ATPase binding / neuron apoptotic process / transmembrane transporter binding / receptor complex / signaling receptor binding / neuronal cell body / positive regulation of cell population proliferation / dendrite / plasma membrane
Similarity search - Function
Transient receptor potential channel, canonical 1 / Transient receptor potential channel, canonical 5 / Transient receptor ion channel domain / Transient receptor ion channel II / Transient receptor ion channel II / Transient receptor potential channel, canonical / Ankyrin repeat / Ankyrin repeats (3 copies) / ankyrin repeats / Ankyrin repeat ...Transient receptor potential channel, canonical 1 / Transient receptor potential channel, canonical 5 / Transient receptor ion channel domain / Transient receptor ion channel II / Transient receptor ion channel II / Transient receptor potential channel, canonical / Ankyrin repeat / Ankyrin repeats (3 copies) / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Short transient receptor potential channel 1 / Short transient receptor potential channel 5
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsKim S-H / Lee HH
Funding support Korea, Republic Of, 1 items
OrganizationGrant numberCountry
Samsung Science and Technology Foundation Korea, Republic Of
CitationJournal: To Be Published
Title: Cryo-EM structure of heteromeric TRPC channel
Authors: Kim S-H / Lee HH
History
DepositionNov 10, 2024-
Header (metadata) releaseNov 12, 2025-
Map releaseNov 12, 2025-
UpdateNov 12, 2025-
Current statusNov 12, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_62343.png

Downloads & links

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Map

FileDownload / File: emd_62343.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.)
0.85 Å/pix.
x 320 pix.
= 271.36 Å		0.85 Å/pix.
x 320 pix.
= 271.36 Å		0.85 Å/pix.
x 320 pix.
= 271.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.848 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.2908512 - 0.46686137
Average (Standard dev.)0.00037786312 (±0.0146143)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 271.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_62343_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_62343_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 : Cryo-EM structure of heteromeric TRPC channel

EntireName: Cryo-EM structure of heteromeric TRPC channel
Components
  • Complex: Cryo-EM structure of heteromeric TRPC channel
    • Protein or peptide: Short transient receptor potential channel 1
    • Protein or peptide: Short transient receptor potential channel 5
  • Ligand: CALCIUM ION
  • Ligand: (2S)-2-(hexadecanoyloxy)-3-hydroxypropyl (9Z)-octadec-9-enoate
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: ZINC ION

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Supramolecule #1: Cryo-EM structure of heteromeric TRPC channel

SupramoleculeName: Cryo-EM structure of heteromeric TRPC channel / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Short transient receptor potential channel 1

MacromoleculeName: Short transient receptor potential channel 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 91.688164 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GPVDMMAALY PSTDLSGASS SSLPSSPSSS SPNEVMALKD VREVKEENTL NEKLFLLACD KGDYYMVKKI LEENSSGDLN INCVDVLGR NAVTITIENE NLDILQLLLD YGCQSADALL VAIDSEVVGA VDILLNHRPK RSSRPTIVKL MERIQNPEYS T TMDVAPVI ...String:
GPVDMMAALY PSTDLSGASS SSLPSSPSSS SPNEVMALKD VREVKEENTL NEKLFLLACD KGDYYMVKKI LEENSSGDLN INCVDVLGR NAVTITIENE NLDILQLLLD YGCQSADALL VAIDSEVVGA VDILLNHRPK RSSRPTIVKL MERIQNPEYS T TMDVAPVI LAAHRNNYEI LTMLLKQDVS LPKPHAVGCE CTLCSAKNKK DSLRHSRFRL DIYRCLASPA LIMLTEEDPI LR AFELSAD LKELSLVEVE FRNDYEELAR QCKMFAKDLL AQARNSRELE VILNHTSSDE PLDKRGLLEE RMNLSRLKLA IKY NQKEFV SQSNCQQFLN TVWFGQMSGY RRKPTCKKIM TVLTVGIFWP VLSLCYLIAP KSQFGRIIHT PFMKFIIHGA SYFT FLLLL NLYSLVYNED KKNTMGPALE RIDYLLILWI IGMIWSDIKR LWYEGLEDFL EESRNQLSFV MNSLYLATFA LKVVA HNKF HDFADRKDWD AFHPTLVAEG LFAFANVLSY LRLFFMYTTS SILGPLQISM GQMLQDFGKF LGMFLLVLFS FTIGLT QLY DKGYTSKEQK DCVGIFCEQQ SNDTFHSFIG TCFALFWYIF SLAHVAIFVT RFSYGEELQS FVGAVIVGTY NVVVVIV LT KLLVAMLHKS FQLIANHEDK EWKFARAKLW LSYFDDKCTL PPPFNIIPSP KTICYMISSL SKWICSHTSK GKVKRQNS L KEWRNLKQKR DENYQKVMCC LVHRYLTSMR QKMQSTDQAT VENLNELRQD LSKFRNEIRD LLGFRTSKYA MFYPRN

UniProtKB: Short transient receptor potential channel 1

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Macromolecule #2: Short transient receptor potential channel 5

MacromoleculeName: Short transient receptor potential channel 5 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 89.951891 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAQLYYKKVN YSPYRDRIPL QIVRAETELS AEEKAFLNAV EKGDYATVKQ ALQEAEIYYN VNINCMDPLG RSALLIAIEN ENLEIMELL LNHSVYVGDA LLYAIRKEVV GAVELLLSYR RPSGEKQVPT LMMDTQFSEF TPDITPIMLA AHTNNYEIIK L LVQKRVTI ...String:
MAQLYYKKVN YSPYRDRIPL QIVRAETELS AEEKAFLNAV EKGDYATVKQ ALQEAEIYYN VNINCMDPLG RSALLIAIEN ENLEIMELL LNHSVYVGDA LLYAIRKEVV GAVELLLSYR RPSGEKQVPT LMMDTQFSEF TPDITPIMLA AHTNNYEIIK L LVQKRVTI PRPHQIRCNC VECVSSSEVD SLRHSRSRLN IYKALASPSL IALSSEDPIL TAFRLGWELK ELSKVENEFK AE YEELSQQ CKLFAKDLLD QARSSRELEI ILNHRDDHSE ELDPQKYHDL AKLKVAIKYH QKEFVAQPNC QQLLATLWYD GFP GWRRKH WVVKLLTCMT IGFLFPMLSI AYLISPRSNL GLFIKKPFIK FICHTASYLT FLFMLLLASQ HIVRTDLHVQ GPPP TVVEW MILPWVLGFI WGEIKEMWDG GFTEYIHDWW NLMDFAMNSL YLATISLKIV AYVKYNGSRP REEWEMWHPT LIAEA LFAI SNILSSLRLI SLFTANSHLG PLQISLGRML LDILKFLFIY CLVLLAFANG LNQLYFYYET RAIDEPNNCK GIRCEK QNN AFSTLFETLQ SLFWSVFGLL NLYVTNVKAR HEFTEFVGAT MFGTYNVISL VVLLNMLIAM MNNSYQLIAD HADIEWK FA RTKLWMSYFD EGGTLPPPFN IIPSPKSFLY LGNWFNNTFC PKRDPDGRRR RRNLRSFTER NADSLIQNQH YQEVIRNL V KRYVAAMIRN SKTHEGLTEE NFKELKQDIS SFRYEVLDLL GNRKSRLEVL FQ

UniProtKB: Short transient receptor potential channel 5

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Macromolecule #3: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 3 / Number of copies: 3 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #4: (2S)-2-(hexadecanoyloxy)-3-hydroxypropyl (9Z)-octadec-9-enoate

MacromoleculeName: (2S)-2-(hexadecanoyloxy)-3-hydroxypropyl (9Z)-octadec-9-enoate
type: ligand / ID: 4 / Number of copies: 3 / Formula: YZY
Molecular weightTheoretical: 594.949 Da
Chemical component information

ChemComp-YZY:
(2S)-2-(hexadecanoyloxy)-3-hydroxypropyl (9Z)-octadec-9-enoate

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Macromolecule #5: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 5 / Number of copies: 3 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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Macromolecule #6: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 6 / Number of copies: 3 / Formula: ZN
Molecular weightTheoretical: 65.409 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 BIOQUANTUM (6k x 4k) / Average electron dose: 66.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7x6c

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 40958
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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