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- EMDB-62060: Cryo-EM structure of the human TRPC1/C5 heteromer -

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Basic information

Entry
Database: EMDB / ID: EMD-62060
TitleCryo-EM structure of the human TRPC1/C5 heteromer
Map data
Sample
  • Complex: Cryo-EM structure of the human TRPC1/C5 heteromer
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,Short transient receptor potential channel 5
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,Short transient receptor potential channel 1,Extended tegument protein pp150
  • Ligand: CALCIUM ION
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: (2S)-2-(hexadecanoyloxy)-3-hydroxypropyl (9Z)-octadec-9-enoate
KeywordsShort transient receptor potential channel 1 / Short transient receptor potential channel 5 / 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 / viral tegument / melanin biosynthetic process / TRP channels / inositol 1,4,5 trisphosphate binding / cation channel complex ...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 / viral tegument / melanin biosynthetic process / TRP channels / inositol 1,4,5 trisphosphate binding / cation channel complex / actinin binding / TRP channels / clathrin binding / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / regulation of cardiac conduction / maltose transport / maltodextrin transmembrane transport / regulation of cytosolic calcium ion concentration / positive regulation of axon extension / monoatomic cation channel activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / Ion homeostasis / calcium channel complex / positive regulation of neuron differentiation / ATP-binding cassette (ABC) transporter complex / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / positive regulation of release of sequestered calcium ion into cytosol / bioluminescence / cell chemotaxis / generation of precursor metabolites and energy / response to calcium ion / calcium ion transmembrane transport / calcium channel activity / neuron differentiation / calcium ion transport / presynapse / outer membrane-bounded periplasmic space / actin binding / positive regulation of cytosolic calcium ion concentration / growth cone / ATPase binding / neuron apoptotic process / transmembrane transporter binding / periplasmic space / receptor complex / signaling receptor binding / neuronal cell body / positive regulation of cell population proliferation / dendrite / DNA damage response / structural molecule activity / membrane / plasma membrane
Similarity search - Function
Transient receptor potential channel, canonical 1 / Herpesvirus UL11/UL32 / Herpesvirus large structural phosphoprotein UL32 / 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 / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site ...Transient receptor potential channel, canonical 1 / Herpesvirus UL11/UL32 / Herpesvirus large structural phosphoprotein UL32 / 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 / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Green fluorescent protein, GFP / Ankyrin repeat / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Ankyrin repeats (3 copies) / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Extended tegument protein pp150 / Maltose/maltodextrin-binding periplasmic protein / Short transient receptor potential channel 1 / Short transient receptor potential channel 5
Similarity search - Component
Biological speciesHomo sapiens (human) / Mus musculus (house mouse) / Human betaherpesvirus 5
Methodsingle particle reconstruction / cryo EM / Resolution: 2.84 Å
AuthorsChen YX / Cheng XY / Zhang J
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of the human TRPC1/C5 heteromer
Authors: Chen YX / Cheng XY
History
DepositionOct 21, 2024-
Header (metadata) releaseOct 22, 2025-
Map releaseOct 22, 2025-
UpdateOct 22, 2025-
Current statusOct 22, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_62060.png

Downloads & links

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Map

FileDownload / File: emd_62060.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 400 pix.
= 332. Å		0.83 Å/pix.
x 400 pix.
= 332. Å		0.83 Å/pix.
x 400 pix.
= 332. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.25724438 - 0.51554954
Average (Standard dev.)0.00023097346 (±0.012855191)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 332.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_62060_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_62060_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 the human TRPC1/C5 heteromer

EntireName: Cryo-EM structure of the human TRPC1/C5 heteromer
Components
  • Complex: Cryo-EM structure of the human TRPC1/C5 heteromer
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,Short transient receptor potential channel 5
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,Short transient receptor potential channel 1,Extended tegument protein pp150
  • Ligand: CALCIUM ION
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: (2S)-2-(hexadecanoyloxy)-3-hydroxypropyl (9Z)-octadec-9-enoate

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Supramolecule #1: Cryo-EM structure of the human TRPC1/C5 heteromer

SupramoleculeName: Cryo-EM structure of the human TRPC1/C5 heteromer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Maltose/maltodextrin-binding periplasmic protein,Short transient ...

MacromoleculeName: Maltose/maltodextrin-binding periplasmic protein,Short transient receptor potential channel 5
type: protein_or_peptide / ID: 1 / Details: Flag-Flag-Flag-MBP-mTRPC5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 136.984219 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGSAGDYKDH DGDYKDHDID YKDDDDKGSA AAMGSSHHHH HHGSSMKIEE GKLVIWINGD KGYNGLAEVG KKFEKDTGIK VTVEHPDKL EEKFPQVAAT GDGPDIIFWA HDRFGGYAQS GLLAEITPDK AFQDKLYPFT WDAVRYNGKL IAYPIAVEAL S LIYNKDLL ...String:
MGSAGDYKDH DGDYKDHDID YKDDDDKGSA AAMGSSHHHH HHGSSMKIEE GKLVIWINGD KGYNGLAEVG KKFEKDTGIK VTVEHPDKL EEKFPQVAAT GDGPDIIFWA HDRFGGYAQS GLLAEITPDK AFQDKLYPFT WDAVRYNGKL IAYPIAVEAL S LIYNKDLL PNPPKTWEEI PALDKELKAK GKSALMFNLQ EPYFTWPLIA ADGGYAFKYE NGKYDIKDVG VDNAGAKAGL TF LVDLIKN KHMNADTDYS IAEAAFNKGE TAMTINGPWA WSNIDTSKVN YGVTVLPTFK GQPSKPFVGV LSAGINAASP NKE LAKEFL ENYLLTDEGL EAVNKDKPLG AVALKSYEEE LAKDPRIAAT MENAQKGEIM PNIPQMSAFW YAVRTAVINA ASGR QTVDE ALKDAQTNSS SNNNNNNNNN NLGIELEVLF QGPMAQLYYK KVNYSPYRDR IPLQIVRAET ELSAEEKAFL SAVEK GDYA TVKQALQEAE IYYNVNINCM DPLGRSALLI AIENENLEIM ELLLNHSVYV GDALLYAIRK EVVGAVELLL SYRKPS GEK QVPTLMMDTQ FSEFTPDITP IMLAAHTNNY EIIKLLVQKR VTIPRPHQIR CNCVECVSSS EVDSLRHSRS RLNIYKA LA SPSLIALSSE DPILTAFRLG WELKELSKVE NEFKAEYEEL SQQCKLFAKD LLDQARSSRE LEIILNHRDD HSEELDPQ K YHDLAKLKVA IKYHQKEFVA QPNCQQLLAT LWYDGFPGWR RKHWVVKLLT CMTIGFLFPM LSIAYLISPR SNLGLFIKK PFIKFICHTA SYLTFLFMLL LASQHIVRTD LHVQGPPPTV VEWMILPWVL GFIWGEIKEM WDGGFTEYIH DWWNLMDFAM NSLYLATIS LKIVAYVKYN GSRPREEWEM WHPTLIAEAL FAISNILSSL RLISLFTANS HLGPLQISLG RMLLDILKFL F IYCLVLLA FANGLNQLYF YYETRAIDEP NNCKGIRCEK QNNAFSTLFE TLQSLFWSVF GLLNLYVTNV KARHEFTEFV GA TMFGTYN VISLVVLLNM LIAMMNNSYQ LIADHADIEW KFARTKLWMS YFDEGGTLPP PFNIIPSPKS FLYLGNWFNN TFC PKRDPD GRRRRHNLRS FTERHADSLI QNQHYQEVIR NLVKRYVAAM IRNSKTNEGL TEENFKELKQ DISSFRYEVL DLLG NRK

UniProtKB: Maltose/maltodextrin-binding periplasmic protein, Short transient receptor potential channel 5

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Macromolecule #2: Maltose/maltodextrin-binding periplasmic protein,Short transient ...

MacromoleculeName: Maltose/maltodextrin-binding periplasmic protein,Short transient receptor potential channel 1,Extended tegument protein pp150
type: protein_or_peptide / ID: 2 / Details: MBP-hTRPC1-GFP-Strep-Strep / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human betaherpesvirus 5
Molecular weightTheoretical: 168.800609 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ATMGMGSSHH HHHHGSSMKI EEGKLVIWIN GDKGYNGLAE VGKKFEKDTG IKVTVEHPDK LEEKFPQVAA TGDGPDIIFW AHDRFGGYA QSGLLAEITP DKAFQDKLYP FTWDAVRYNG KLIAYPIAVE ALSLIYNKDL LPNPPKTWEE IPALDKELKA K GKSALMFN ...String:
ATMGMGSSHH HHHHGSSMKI EEGKLVIWIN GDKGYNGLAE VGKKFEKDTG IKVTVEHPDK LEEKFPQVAA TGDGPDIIFW AHDRFGGYA QSGLLAEITP DKAFQDKLYP FTWDAVRYNG KLIAYPIAVE ALSLIYNKDL LPNPPKTWEE IPALDKELKA K GKSALMFN LQEPYFTWPL IAADGGYAFK YENGKYDIKD VGVDNAGAKA GLTFLVDLIK NKHMNADTDY SIAEAAFNKG ET AMTINGP WAWSNIDTSK VNYGVTVLPT FKGQPSKPFV GVLSAGINAA SPNKELAKEF LENYLLTDEG LEAVNKDKPL GAV ALKSYE EELAKDPRIA ATMENAQKGE IMPNIPQMSA FWYAVRTAVI NAASGRQTVD EALKDAQTNS SSNNNNNNNN NNLG IELEV LFQGPMMAAL YPSTDLSGAS SSSLPSSPSS SSPNEVMALK DVREVKEENT LNEKLFLLAC DKGDYYMVKK ILEEN SSGD LNINCVDVLG RNAVTITIEN ENLDILQLLL DYGCQSADAL LVAIDSEVVG AVDILLNHRP KRSSRPTIVK LMERIQ NPE YSTTMDVAPV ILAAHRNNYE ILTMLLKQDV SLPKPHAVGC ECTLCSAKNK KDSLRHSRFR LDIYRCLASP ALIMLTE ED PILRAFELSA DLKELSLVEV EFRNDYEELA RQCKMFAKDL LAQARNSREL EVILNHTSSD EPLDKRGLLE ERMNLSRL K LAIKYNQKEF VSQSNCQQFL NTVWFGQMSG YRRKPTCKKI MTVLTVGIFW PVLSLCYLIA PKSQFGRIIH TPFMKFIIH GASYFTFLLL LNLYSLVYNE DKKNTMGPAL ERIDYLLILW IIGMIWSDIK RLWYEGLEDF LEESRNQLSF VMNSLYLATF ALKVVAHNK FHDFADRKDW DAFHPTLVAE GLFAFANVLS YLRLFFMYTT SSILGPLQIS MGQMLQDFGK FLGMFLLVLF S FTIGLTQL YDKGYTSKEQ KDCVGIFCEQ QSNDTFHSFI GTCFALFWYI FSLAHVAIFV TRFSYGEELQ SFVGAVIVGT YN VVVVIVL TKLLVAMLHK SFQLIANHED KEWKFARAKL WLSYFDDKCT LPPPFNIIPS PKTICYMISS LSKWICSHTS KGK VKRQNS LKEWRNLKQK RDENYQKVMC CLVHRYLTSM RQKMQSTDQA TVENLNELRQ DLSKFRNEIR DLLGFRTSKY AMFY PRNGG GSGGGSGGGS ENLYFQGGSA GSAMVSKGEE LFTGVVPILV ELDGDVNGHK FSVSGEGEGD ATYGKLTLKF ICTTG KLPV PWPTLVTTLT YGVQCFSRYP DHMKQHDFFK SAMPEGYVQE RTIFFKDDGN YKTRAEVKFE GDTLVNRIEL KGIDFK EDG NILGHKLEYN YNSHNVYIMA DKQKNGIKVN FKIRHNIEDG SVQLADHYQQ NTPIGDGPVL LPDNHYLSTQ SALSKDP NE KRDHMVLLEF VTAAGITLGM DELYKGSAGS AGSAWSHPQF EKGGGSGGGS GGGSWSHPQF EK

UniProtKB: Maltose/maltodextrin-binding periplasmic protein, Short transient receptor potential channel 1, Extended tegument protein pp150

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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: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 4 / Number of copies: 3 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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Macromolecule #5: (2S)-2-(hexadecanoyloxy)-3-hydroxypropyl (9Z)-octadec-9-enoate

MacromoleculeName: (2S)-2-(hexadecanoyloxy)-3-hydroxypropyl (9Z)-octadec-9-enoate
type: ligand / ID: 5 / Number of copies: 4 / 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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F30
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 54.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: 4D-STEM / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Tecnai F30 / 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: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 143788
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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