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- EMDB-65025: Structure of hTRPC3 solubilized with 4F peptide at 2.72 angstrom -

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Basic information

Entry
Database: EMDB / ID: EMD-65025
TitleStructure of hTRPC3 solubilized with 4F peptide at 2.72 angstrom
Map data
Sample
  • Complex: TRPC3 tetramer solubilized with 4F peptide
    • Protein or peptide: Green fluorescence protein,Maltose/maltodextrin-binding periplasmic protein,Short transient receptor potential channel 3,Maltose/maltodextrin-binding periplasmic protein,Short transient receptor potential channel 3,Maltose/maltodextrin-binding periplasmic protein,Short transient receptor potential channel 3
  • Ligand: CALCIUM ION
  • Ligand: ZINC ION
  • Ligand: [(2~{S})-2-[(~{E})-octadec-9-enoyl]oxy-3-oxidanyl-propyl] octadec-9-enoate
  • Ligand: water
KeywordsTRPC3 / 4F peptide / native lipid environment / METAL TRANSPORT
Function / homology
Function and homology information


positive regulation of cardiac muscle hypertrophy in response to stress / Role of second messengers in netrin-1 signaling / store-operated calcium channel activity / Effects of PIP2 hydrolysis / Elevation of cytosolic Ca2+ levels / cation channel complex / inositol 1,4,5 trisphosphate binding / calcium-activated cation channel activity / single fertilization / response to ATP ...positive regulation of cardiac muscle hypertrophy in response to stress / Role of second messengers in netrin-1 signaling / store-operated calcium channel activity / Effects of PIP2 hydrolysis / Elevation of cytosolic Ca2+ levels / cation channel complex / inositol 1,4,5 trisphosphate binding / calcium-activated cation channel activity / single fertilization / response to ATP / TRP channels / positive regulation of calcium ion transport into cytosol / phototransduction / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / regulation of cytosolic calcium ion concentration / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / MECP2 regulates neuronal receptors and channels / response to calcium ion / calcium ion transmembrane transport / calcium channel activity / calcium ion transport / outer membrane-bounded periplasmic space / 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 / : / Calcium channel YVC1-like, C-terminal / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. ...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 / : / Calcium channel YVC1-like, C-terminal / 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 / Ankyrin repeats (3 copies) / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily
Similarity search - Domain/homology
Maltose/maltodextrin-binding periplasmic protein / Short transient receptor potential channel 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.72 Å
AuthorsChen L / Zang J
Funding support China, 2 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2022YFA1303000 China
National Natural Science Foundation of China (NSFC)32225027 China
CitationJournal: J Mol Biol / Year: 2025
Title: Unveiling Eukaryotic Membrane Proteins in High Resolution Using Peptide Solubilization.
Authors: Jiahe Zang / Yiting Shi / Weiyu Tao / Xiaoyu Liu / Wenjun Guo / Lei Chen /
Abstract: Integral membrane proteins are vital for numerous biological functions and their structures are typically studied using X-ray crystallography and cryo-electron microscopy (cryo-EM). However, these ...Integral membrane proteins are vital for numerous biological functions and their structures are typically studied using X-ray crystallography and cryo-electron microscopy (cryo-EM). However, these techniques require the extraction of target membrane proteins from their native membranes using detergents, which might disrupt the lipid environments and alter protein behavior. In this study, we present a novel method for solubilizing membrane proteins using 4F peptide, thereby eliminating the need for detergents throughout the procedure. We demonstrate that the 4F peptide effectively solubilizes a range of membrane proteins and complexes into 4F-discs, while preserving their functionality and structural integrity. Converting these 4F-discs into nanodiscs further enhances particle homogeneity and facilitates high-resolution structural determination of membrane proteins. Our findings highlight the potential of membrane-solubilizing peptides to advance membrane protein research.
History
DepositionJun 11, 2025-
Header (metadata) releaseApr 22, 2026-
Map releaseApr 22, 2026-
UpdateApr 22, 2026-
Current statusApr 22, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_65025.png

Downloads & links

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Map

FileDownload / File: emd_65025.map.gz / Format: CCP4 / Size: 149.9 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 340 pix.
= 283.56 Å		0.83 Å/pix.
x 340 pix.
= 283.56 Å		0.83 Å/pix.
x 340 pix.
= 283.56 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.834 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.38
Minimum - Maximum-1.8626448 - 3.1207075
Average (Standard dev.)0.0053158333 (±0.104198046)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 283.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_65025_msk_1.map
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Additional map: #1

Fileemd_65025_additional_1.map
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Half map: #2

Fileemd_65025_half_map_1.map
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Half map: #1

Fileemd_65025_half_map_2.map
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Sample components

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Entire : TRPC3 tetramer solubilized with 4F peptide

EntireName: TRPC3 tetramer solubilized with 4F peptide
Components
  • Complex: TRPC3 tetramer solubilized with 4F peptide
    • Protein or peptide: Green fluorescence protein,Maltose/maltodextrin-binding periplasmic protein,Short transient receptor potential channel 3,Maltose/maltodextrin-binding periplasmic protein,Short transient receptor potential channel 3,Maltose/maltodextrin-binding periplasmic protein,Short transient receptor potential channel 3
  • Ligand: CALCIUM ION
  • Ligand: ZINC ION
  • Ligand: [(2~{S})-2-[(~{E})-octadec-9-enoyl]oxy-3-oxidanyl-propyl] octadec-9-enoate
  • Ligand: water

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Supramolecule #1: TRPC3 tetramer solubilized with 4F peptide

SupramoleculeName: TRPC3 tetramer solubilized with 4F peptide / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Green fluorescence protein,Maltose/maltodextrin-binding periplasm...

MacromoleculeName: Green fluorescence protein,Maltose/maltodextrin-binding periplasmic protein,Short transient receptor potential channel 3,Maltose/maltodextrin-binding periplasmic protein,Short transient ...Name: Green fluorescence protein,Maltose/maltodextrin-binding periplasmic protein,Short transient receptor potential channel 3,Maltose/maltodextrin-binding periplasmic protein,Short transient receptor potential channel 3,Maltose/maltodextrin-binding periplasmic protein,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: 173.36025 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSKGEELFTG VVPILVELDG DVNGHKFSVR GEGEGDATIG KLTLKFISTT GKLPVPWPTL VTTLTYGVQC FSRYPDHMKR HDFFKSAMP EGYVQERTIS FKDDGKYKTR AVVKFEGDTL VNRIELKGTD FKEDGNILGH KLEYNFNSHN VYITADKQKN G IKANFTVR ...String:
MSKGEELFTG VVPILVELDG DVNGHKFSVR GEGEGDATIG KLTLKFISTT GKLPVPWPTL VTTLTYGVQC FSRYPDHMKR HDFFKSAMP EGYVQERTIS FKDDGKYKTR AVVKFEGDTL VNRIELKGTD FKEDGNILGH KLEYNFNSHN VYITADKQKN G IKANFTVR HNVEGSGHHH HHHHHHHHHS SGLVPRGSGW SHPQFEKGSG DYKDDDDKGS GWSHPQFEKG SGDGSVQLAD HY QQNTPIG DGPVLLPDNH YLSTQTVLSK DPNEKRDHMV LLEFVTAAGI THGMDELYKG SMKIEEGKLV IWINGDKGYN GLA EVGKKF EKDTGIKVTV EHPDKLEEKF PQVAATGDGP DIIFWAHDRF GGYAQSGLLA EITPDKAFQD KLYPFTWDAV RYNG KLIAY PIAVEALSLI YNKDLLPNPP KTWEEIPALD KELKAKGKSA LMFNLQEPYF TWPLIAADGG YAFKYENGKY DIKDV GVDN AGAKAGLTFL VDLIKNKHMN ADTDYSIAEA AFNKGETAMT INGPWAWSNI DTSKVNYGVT VLPTFKGQPS KPFVGV LSA GINAASPNKE LAKEFLENYL LTDEGLEAVN KDKPLGAVAL KSYEEELVKD PRIAATMENA QKGEIMPNIP QMSAFWY AV RTAVINAASG RQTVDEALKD AQTGGLEVLF QGPEFGLNDI FEAQKIEWHE GSGSGSMREK GRRQAVRGPA FMFNDRGT S LTAEEERFLD AAEYGNIPVV RKMLEESKTL NVNCVDYMGQ NALQLAVGNE HLEVTELLLK KENLARIGDA LLLAISKGY VRIVEAILNH PGFAASKRLT LSPCEQELQD DDFYAYDEDG TRFSPDITPI ILAAHCQKYE VVHMLLMKGA RIERPHDYFC KCGDCMEKQ RHDSFSHSRS RINAYKGLAS PAYLSLSSED PVLTALELSN ELAKLANIEK EFKNDYRKLS MQCKDFVVGV L DLCRDSEE VEAILNGDLE SAEPLEVHRH KASLSRVKLA IKYEVKKFVA HPNCQQQLLT IWYENLSGLR EQTIAIKCLV VL VVALGLP FLAIGYWIAP CSRLGKILRS PFMKFVAHAA SFIIFLGLLV FNASDRFEGI TTLPNITVTD YPKQIFRVKT TQF TWTEML IMVWVLGMMW SECKELWLEG PREYILQLWN VLDFGMLSIF IAAFTARFLA FLQATKAQQY VDSYVQESDL SEVT LPPEI QYFTYARDKW LPSDPQIISE GLYAIAVVLS FSRIAYILPA NESFGPLQIS LGRTVKDIFK FMVLFIMVFF AFMIG MFIL YSYYLGAKVN AAFTTVEESF KTLFWSIFGL SEVTSVVLKY DHKFIENIGY VLYGIYNVTM VVVLLNMLIA MINSSY QEI EDDSDVEWKF ARSKLWLSYF DDGKTLPPPF SLVPSPKSFV YFIMRIVNFP KCRRRRLQKD IEMGMGNSKS RLNLFTQ SN SRVFESHSFN SILNQPTRYQ QIMKRLIKRY VLKAQVDKEN DEVNEGELKE IKQDISSLRY ELLEDKSQAT EELAILIH K LSEKLNPSML RCE

UniProtKB: Maltose/maltodextrin-binding periplasmic protein, Short transient receptor potential channel 3

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Macromolecule #2: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 8 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 4 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #4: [(2~{S})-2-[(~{E})-octadec-9-enoyl]oxy-3-oxidanyl-propyl] octadec...

MacromoleculeName: [(2~{S})-2-[(~{E})-octadec-9-enoyl]oxy-3-oxidanyl-propyl] octadec-9-enoate
type: ligand / ID: 4 / Number of copies: 4 / Formula: A1L5I
Molecular weightTheoretical: 620.986 Da

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 32 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 591309
CTF correctionType: NONE
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.72 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 65480
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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