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- PDB-9khi: Cryo-EM structure of heteromeric TRPC channel -

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Basic information

Entry
Database: PDB / ID: 9khi
TitleCryo-EM structure of heteromeric TRPC channel
Components(Short transient receptor potential channel ...) x 2
KeywordsMEMBRANE PROTEIN / TRP
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 / positive regulation of neuron differentiation / calcium channel complex / 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 / actin binding / growth cone / positive regulation of cytosolic calcium ion concentration / 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
CHOLESTEROL HEMISUCCINATE / Chem-YZY / Short transient receptor potential channel 1 / Short transient receptor potential channel 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsKim, S.-H. / Lee, H.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Samsung Science and Technology Foundation Korea, Republic Of
CitationJournal: Nat Commun / Year: 2025
Title: Molecular architecture of the human TRPC1/C5 heteromeric channel.
Authors: Sun-Hong Kim / Hyunwoo Park / Jinhyeong Kim / Hana Kang / Jongdae Won / Byoung-Cheol Lee / Insuk So / Hyung Ho Lee /
Abstract: Transient receptor potential (TRP) ion channels form heteromers through combinatorial associations of distinct subunits, contributing to the diversity of TRP channel functions. Among them, TRPC5, ...Transient receptor potential (TRP) ion channels form heteromers through combinatorial associations of distinct subunits, contributing to the diversity of TRP channel functions. Among them, TRPC5, which forms a heteromer with TRPC1, represents an attractive pharmaceutical target for treating anxiety and depression. Here, we present the cryo-electron microscopy structure of the human TRPC1/C5 heteromer, composed of one TRPC1 subunit and three TRPC5 subunits. The incorporation of TRPC1 into the heteromer disrupts the C symmetry of the TRPC5 homotetramer, resulting in a distinct ion conduction pathway characterized by an asymmetrically constricted selectivity filter and an asymmetric lower gate. The TRPC1/C5 heteromer displays recognizable structural features compared to the TRPC1/C4 heteromer, including a noncanonically tilted coiled-coil domain and a distinct intersubunit interactions. Furthermore, we elucidate the structures of human TRPC5 bound to the TRPC1/4/5-specific agonist, (-)-Englerin A. Our findings establish a foundation for exploring the diversity of heteromeric TRP channels and pave the way for targeting TRPC1/C5 as a therapeutic strategy.
History
DepositionNov 10, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 12, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Short transient receptor potential channel 1
D: Short transient receptor potential channel 5
C: Short transient receptor potential channel 5
B: Short transient receptor potential channel 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)365,10516
Polymers361,5444
Non-polymers3,56112
Water00
1


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

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Components

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Short transient receptor potential channel ... , 2 types, 4 molecules ADCB

#1: Protein Short transient receptor potential channel 1 / TrpC1 / Transient receptor protein 1 / TRP-1


Mass: 91688.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRPC1, TRP1 / Production host: Homo sapiens (human) / References: UniProt: P48995
#2: Protein Short transient receptor potential channel 5 / TrpC5 / Transient receptor protein 5 / TRP-5 / hTRP-5 / hTRP5


Mass: 89951.891 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRPC5, TRP5 / Production host: Homo sapiens (human) / References: UniProt: Q9UL62

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Non-polymers , 4 types, 12 molecules

#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-YZY / (2S)-2-(hexadecanoyloxy)-3-hydroxypropyl (9Z)-octadec-9-enoate


Mass: 594.949 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C37H70O5 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-Y01 / CHOLESTEROL HEMISUCCINATE


Mass: 486.726 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C31H50O4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Details

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 heteromeric TRPC channel / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightExperimental value: NO
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: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 66.8 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 40958 / Symmetry type: POINT
RefinementHighest resolution: 2.7 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00221963
ELECTRON MICROSCOPYf_angle_d0.45729713
ELECTRON MICROSCOPYf_dihedral_angle_d8.4422946
ELECTRON MICROSCOPYf_chiral_restr0.0353363
ELECTRON MICROSCOPYf_plane_restr0.0043675

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