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- PDB-6aei: Cryo-EM structure of the receptor-activated TRPC5 ion channel -

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Basic information

Entry
Database: PDB / ID: 6aei
TitleCryo-EM structure of the receptor-activated TRPC5 ion channel
ComponentsShort transient receptor potential channel 5
KeywordsMEMBRANE PROTEIN / Cryo-EM / mouse TRPC5 / ion channel
Function / homology
Function and homology information


regulation of membrane hyperpolarization / phosphatidylserine exposure on apoptotic cell surface / negative regulation of dendrite morphogenesis / store-operated calcium channel activity / cation channel complex / TRP channels / inositol 1,4,5 trisphosphate binding / actinin binding / clathrin binding / positive regulation of axon extension ...regulation of membrane hyperpolarization / phosphatidylserine exposure on apoptotic cell surface / negative regulation of dendrite morphogenesis / store-operated calcium channel activity / cation channel complex / TRP channels / inositol 1,4,5 trisphosphate binding / actinin binding / clathrin binding / positive regulation of axon extension / regulation of cytosolic calcium ion concentration / calcium channel complex / positive regulation of neuron differentiation / positive regulation of peptidyl-threonine phosphorylation / calcium ion transmembrane transport / neuron differentiation / presynapse / actin binding / ATPase binding / positive regulation of cytosolic calcium ion concentration / growth cone / neuron apoptotic process / neuronal cell body / dendrite / positive regulation of cell population proliferation / plasma membrane
Similarity search - Function
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 ...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
Chem-LPP / CHOLESTEROL HEMISUCCINATE / Short transient receptor potential channel 5
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.89 Å
AuthorsDuan, J. / Li, Z. / Li, J. / Zhang, J.
CitationJournal: Sci Adv / Year: 2019
Title: Cryo-EM structure of TRPC5 at 2.8-Å resolution reveals unique and conserved structural elements essential for channel function.
Authors: Jingjing Duan / Jian Li / Gui-Lan Chen / Yan Ge / Jieyu Liu / Kechen Xie / Xiaogang Peng / Wei Zhou / Jianing Zhong / Yixing Zhang / Jie Xu / Changhu Xue / Bo Liang / Lan Zhu / Wei Liu / ...Authors: Jingjing Duan / Jian Li / Gui-Lan Chen / Yan Ge / Jieyu Liu / Kechen Xie / Xiaogang Peng / Wei Zhou / Jianing Zhong / Yixing Zhang / Jie Xu / Changhu Xue / Bo Liang / Lan Zhu / Wei Liu / Cheng Zhang / Xiao-Li Tian / Jianbin Wang / David E Clapham / Bo Zeng / Zongli Li / Jin Zhang /
Abstract: The transient receptor potential canonical subfamily member 5 (TRPC5), one of seven mammalian TRPC members, is a nonselective calcium-permeant cation channel. TRPC5 is of considerable interest as a ...The transient receptor potential canonical subfamily member 5 (TRPC5), one of seven mammalian TRPC members, is a nonselective calcium-permeant cation channel. TRPC5 is of considerable interest as a drug target in the treatment of progressive kidney disease, depression, and anxiety. Here, we present the 2.8-Å resolution cryo-electron microscopy (cryo-EM) structure of the mouse TRPC5 (mTRPC5) homotetramer. Comparison of the TRPC5 structure to previously determined structures of other TRPC and TRP channels reveals differences in the extracellular pore domain and in the length of the S3 helix. The disulfide bond at the extracellular side of the pore and a preceding small loop are essential elements for its proper function. This high-resolution structure of mTRPC5, combined with electrophysiology and mutagenesis, provides insight into the lipid modulation and gating mechanisms of the TRPC family of ion channels.
History
DepositionAug 5, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)360,27217
Polymers355,6154
Non-polymers4,65713
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area41380 Å2
ΔGint-361 kcal/mol
Surface area114860 Å2

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Components

#1: Protein
Short transient receptor potential channel 5 / TrpC5 / Capacitative calcium entry channel 2 / CCE2 / Transient receptor protein 5 / mTRP5 / Trp- ...TrpC5 / Capacitative calcium entry channel 2 / CCE2 / Transient receptor protein 5 / mTRP5 / Trp-related protein 5


Mass: 88903.672 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Trpc5, Trp5, Trrp5 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9QX29
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-Y01 / CHOLESTEROL HEMISUCCINATE


Mass: 486.726 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C31H50O4
#4: Chemical
ChemComp-LPP / 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE / 1,2-DIPALMITOYL-SN-GLYCERO-3-PHOSPHATE / L-B,G-DIPALMITOYL-A-PHOSPHATIDIC ACID DISODIUM SALT / 3-SN-PHOSPHATIDIC ACID / 1,2-DIPALMITOYLDISODIUM SALT


Mass: 648.891 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C35H69O8P / Comment: phospholipid*YM
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: Mouse TRPC5 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
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 Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 42.3 e/Å2 / Film or detector model: GATAN K2 IS (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1164065 / Num. of class averages: 340465 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00621340
ELECTRON MICROSCOPYf_angle_d0.92328940
ELECTRON MICROSCOPYf_dihedral_angle_d9.78712660
ELECTRON MICROSCOPYf_chiral_restr0.0553268
ELECTRON MICROSCOPYf_plane_restr0.0083600

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