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- PDB-9k4i: Cryo-EM structure of the human TRPC1/C5 heteromer -

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Basic information

Entry
Database: PDB / ID: 9k4i
TitleCryo-EM structure of the human TRPC1/C5 heteromer
Components
  • Maltose/maltodextrin-binding periplasmic protein,Short transient receptor potential channel 1,Extended tegument protein pp150
  • Maltose/maltodextrin-binding periplasmic protein,Short transient receptor potential channel 5
KeywordsMEMBRANE PROTEIN / Short transient receptor potential channel 1 / Short transient receptor potential channel 5
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
CHOLESTEROL HEMISUCCINATE / Chem-YZY / 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 speciesEscherichia coli (E. coli)
Mus musculus (house mouse)
Escherichia coli K-12 (bacteria)
Homo sapiens (human)
Human betaherpesvirus 5
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.84 Å
AuthorsChen, Y.X. / Cheng, X.Y. / Zhang, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of the human TRPC1/C5 heteromer
Authors: Chen, Y.X. / Cheng, X.Y.
History
DepositionOct 21, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Maltose/maltodextrin-binding periplasmic protein,Short transient receptor potential channel 5
B: Maltose/maltodextrin-binding periplasmic protein,Short transient receptor potential channel 1,Extended tegument protein pp150
C: Maltose/maltodextrin-binding periplasmic protein,Short transient receptor potential channel 5
D: Maltose/maltodextrin-binding periplasmic protein,Short transient receptor potential channel 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)583,71314
Polymers579,7534
Non-polymers3,96010
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Maltose/maltodextrin-binding periplasmic protein,Short transient receptor potential channel 5 / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / TrpC5 / Capacitative calcium ...MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / TrpC5 / Capacitative calcium entry channel 2 / CCE2 / Transient receptor protein 5 / TRP-5 / mTRP5 / Trp-related protein 5


Mass: 136984.219 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: Flag-Flag-Flag-MBP-mTRPC5
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) Mus musculus (house mouse)
Gene: malE, b4034, JW3994, Trpc5, Trp5, Trrp5 / Production host: Homo sapiens (human) / References: UniProt: P0AEX9, UniProt: Q9QX29
#2: Protein Maltose/maltodextrin-binding periplasmic protein,Short transient receptor potential channel 1,Extended tegument protein pp150 / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / TrpC1 / Transient receptor ...MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / TrpC1 / Transient receptor protein 1 / TRP-1


Mass: 168800.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: MBP-hTRPC1-GFP-Strep-Strep
Source: (gene. exp.) Escherichia coli K-12 (bacteria), (gene. exp.) Homo sapiens (human), (gene. exp.) Human betaherpesvirus 5
Gene: malE, b4034, JW3994, TRPC1, TRP1, UL32 / Production host: Homo sapiens (human)
References: UniProt: P0AEX9, UniProt: P48995, UniProt: A0A076JQ90
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-Y01 / CHOLESTEROL HEMISUCCINATE


Mass: 486.726 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C31H50O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-YZY / (2S)-2-(hexadecanoyloxy)-3-hydroxypropyl (9Z)-octadec-9-enoate


Mass: 594.949 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C37H70O5 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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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: Cryo-EM structure of the human TRPC1/C5 heteromer / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
11Homo sapiens (human)9606
21Mus musculus (house mouse)10090
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
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: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: 4D-STEM / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 54 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 143788 / Symmetry type: POINT

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