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- PDB-8wpm: Cryo-EM structure of the human TRPC1/C4 heteromer in complex with... -

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Basic information

Entry
Database: PDB / ID: 8wpm
TitleCryo-EM structure of the human TRPC1/C4 heteromer in complex with Pico145
Components
  • Short transient receptor potential channel 1
  • Short transient receptor potential channel 4
KeywordsMETAL TRANSPORT / transient receptor potential
Function / homology
Function and homology information


Role of second messengers in netrin-1 signaling / gamma-aminobutyric acid secretion / store-operated calcium channel activity / melanin biosynthetic process / inositol 1,4,5 trisphosphate binding / cation channel complex / calcium ion import / TRP channels / cortical cytoskeleton / oligodendrocyte differentiation ...Role of second messengers in netrin-1 signaling / gamma-aminobutyric acid secretion / store-operated calcium channel activity / melanin biosynthetic process / inositol 1,4,5 trisphosphate binding / cation channel complex / calcium ion import / TRP channels / cortical cytoskeleton / oligodendrocyte differentiation / regulation of cardiac conduction / regulation of cytosolic calcium ion concentration / monoatomic cation channel activity / Ion homeostasis / 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 / beta-catenin binding / calcium ion transmembrane transport / caveola / calcium channel activity / response to calcium ion / calcium ion transport / ATPase binding / basolateral plasma membrane / transmembrane transporter binding / receptor complex / cadherin binding / signaling receptor binding / cell surface / plasma membrane
Similarity search - Function
Transient receptor potential channel, canonical 1 / Transient receptor potential channel, canonical 4 / 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 repeat profile. / Ankyrin repeat region circular profile. ...Transient receptor potential channel, canonical 1 / Transient receptor potential channel, canonical 4 / 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 repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Chem-PJQ / Short transient receptor potential channel 1 / Short transient receptor potential channel 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.43 Å
AuthorsWon, J. / Jeong, H. / Lee, H.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Other privateSSTF-BA2101-13 Korea, Republic Of
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Cryo-EM structure of the heteromeric TRPC1/TRPC4 channel.
Authors: Jongdae Won / Jinhyeong Kim / Jinsung Kim / Juyeon Ko / Christine Haewon Park / Byeongseok Jeong / Sang-Eun Lee / Hyeongseop Jeong / Sun-Hong Kim / Hyunwoo Park / Insuk So / Hyung Ho Lee /
Abstract: Transient receptor potential (TRP) ion channels have a crucial role as cellular sensors, mediating diverse physical and chemical stimuli. The formation of heteromeric structures expands the ...Transient receptor potential (TRP) ion channels have a crucial role as cellular sensors, mediating diverse physical and chemical stimuli. The formation of heteromeric structures expands the functionality of TRP channels; however, their molecular architecture remains largely unknown. Here we present the cryo-electron microscopy structures of the human TRPC1/TRPC4 heteromer in the apo and antagonist-bound states, both consisting of one TRPC1 subunit and three TRPC4 subunits. The heteromer structure reveals a distinct ion-conduction pathway, including an asymmetrically constricted selectivity filter and an asymmetric lower gate, primarily attributed to the incorporation of TRPC1. Through a structure-guided electrophysiological assay, we show that both the selectivity filter and the lower part of the S6 helix participate in deciding overall preference for permeating monovalent cations. Moreover, we reveal that the introduction of one lysine residue of TRPC1 into the tetrameric central cavity is enough to render one of the most important functional consequences of TRPC heteromerization: reduced calcium permeability. Our results establish a framework for addressing the structure-function relationship of the heteromeric TRP channels.
History
DepositionOct 10, 2023Deposition site: PDBJ / Processing site: PDBJ
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Short transient receptor potential channel 1
B: Short transient receptor potential channel 4
C: Short transient receptor potential channel 4
D: Short transient receptor potential channel 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)409,64315
Polymers407,1624
Non-polymers2,48111
Water00
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 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
Details: GPVD (1-4) linker / Source: (gene. exp.) Homo sapiens (human) / Gene: TRPC1, TRP1 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P48995
#2: Protein Short transient receptor potential channel 4 / TrpC4 / Trp-related protein 4 / hTrp-4 / hTrp4


Mass: 105157.977 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: SRASTVPRARDPPVATLEVLFQ (894-915), linker / Source: (gene. exp.) Homo sapiens (human) / Gene: TRPC4 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q9UBN4
#3: Chemical
ChemComp-PJQ / 7-[(4-chlorophenyl)methyl]-3-methyl-1-(3-oxidanylpropyl)-8-[3-(trifluoromethyloxy)phenoxy]purine-2,6-dione


Mass: 524.877 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C23H20ClF3N4O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca / 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: Structure of a TRP channel complex, apo state / 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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1700 nm / Nominal defocus min: 700 nm
Image recordingElectron dose: 67.7 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.43 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 51926 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00522523
ELECTRON MICROSCOPYf_angle_d0.78130504
ELECTRON MICROSCOPYf_dihedral_angle_d5.0042932
ELECTRON MICROSCOPYf_chiral_restr0.0443420
ELECTRON MICROSCOPYf_plane_restr0.0073803

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