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- PDB-9vfi: Structure of hTRPC3 solubilized with 4F peptide at 2.72 angstrom -

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Basic information

Entry
Database: PDB / ID: 9vfi
TitleStructure of hTRPC3 solubilized with 4F peptide at 2.72 angstrom
ComponentsGreen 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
KeywordsMETAL TRANSPORT / TRPC3 / 4F peptide / native lipid environment
Function / homology
Function and homology information


positive regulation of cardiac muscle hypertrophy in response to stress / Effects of PIP2 hydrolysis / Role of second messengers in netrin-1 signaling / store-operated calcium channel activity / 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 cardiac muscle hypertrophy in response to stress / Effects of PIP2 hydrolysis / Role of second messengers in netrin-1 signaling / store-operated calcium channel activity / Elevation of cytosolic Ca2+ levels / inositol 1,4,5 trisphosphate binding / cation channel complex / calcium-activated cation channel activity / TRP channels / response to ATP / phototransduction / positive regulation of calcium ion transport into cytosol / carbohydrate transmembrane transporter activity / maltose binding / single fertilization / maltose transport / maltodextrin transmembrane transport / regulation of cytosolic calcium ion concentration / MECP2 regulates neuronal receptors and channels / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / 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 / 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 ...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 / 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 / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
: / Maltose/maltodextrin-binding periplasmic protein / Short transient receptor potential channel 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.72 Å
AuthorsChen, L. / Zang, J.
Funding support China, 2items
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, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 22, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: 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
B: 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
C: 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
D: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)696,50720
Polymers693,4414
Non-polymers3,06616
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
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 / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / TrpC3 / Transient receptor ...MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / TrpC3 / Transient receptor protein 3 / TRP-3 / hTrp-3 / hTrp3


Mass: 173360.250 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BTE48_16205, malE, Z5632, ECs5017, TRPC3, TRP3 / Production host: Homo sapiens (human) / References: UniProt: P0AEY0, UniProt: Q13507
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-A1L5I / [(2~{S})-2-[(~{E})-octadec-9-enoyl]oxy-3-oxidanyl-propyl] octadec-9-enoate


Mass: 620.986 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C39H72O5 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: TRPC3 tetramer solubilized with 4F peptide / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 591309
3D reconstructionResolution: 2.72 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 65480 / Symmetry type: POINT

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