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- PDB-5z96: Structure of the mouse TRPC4 ion channel -

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Basic information

Entry
Database: PDB / ID: 5z96
TitleStructure of the mouse TRPC4 ion channel
ComponentsShort transient receptor potential channel 4
KeywordsMEMBRANE PROTEIN / CryoEM / mouse full length TRPC4
Function / homology
Function and homology information


regulation of action potential firing rate / positive regulation of store-operated calcium entry / gamma-aminobutyric acid secretion / store-operated calcium channel activity / cation channel complex / TRP channels / inositol 1,4,5 trisphosphate binding / calcium ion import / cortical cytoskeleton / oligodendrocyte differentiation ...regulation of action potential firing rate / positive regulation of store-operated calcium entry / gamma-aminobutyric acid secretion / store-operated calcium channel activity / cation channel complex / TRP channels / inositol 1,4,5 trisphosphate binding / calcium ion import / cortical cytoskeleton / oligodendrocyte differentiation / regulation of calcium ion transport / calcium channel complex / regulation of cytosolic calcium ion concentration / caveola / calcium ion transmembrane transport / calcium channel activity / beta-catenin binding / calcium ion transport / cell-cell junction / basolateral plasma membrane / cadherin binding / membrane raft / cell surface / protein-containing complex / plasma membrane
Similarity search - Function
Transient receptor potential channel, canonical 4 / Transient receptor ion channel II / Transient receptor ion channel domain / 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 ...Transient receptor potential channel, canonical 4 / Transient receptor ion channel II / Transient receptor ion channel domain / 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-LPP / CHOLESTEROL HEMISUCCINATE / Short transient receptor potential channel 4
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.28 Å
AuthorsDuan, J. / Li, Z. / Li, J. / Zhang, J.
CitationJournal: Nat Commun / Year: 2018
Title: Structure of the mouse TRPC4 ion channel.
Authors: Jingjing Duan / Jian Li / Bo Zeng / Gui-Lan Chen / Xiaogang Peng / Yixing Zhang / Jianbin Wang / David E Clapham / Zongli Li / Jin Zhang /
Abstract: Members of the transient receptor potential (TRP) ion channels conduct cations into cells. They mediate functions ranging from neuronally mediated hot and cold sensation to intracellular organellar ...Members of the transient receptor potential (TRP) ion channels conduct cations into cells. They mediate functions ranging from neuronally mediated hot and cold sensation to intracellular organellar and primary ciliary signaling. Here we report a cryo-electron microscopy (cryo-EM) structure of TRPC4 in its unliganded (apo) state to an overall resolution of 3.3 Å. The structure reveals a unique architecture with a long pore loop stabilized by a disulfide bond. Beyond the shared tetrameric six-transmembrane fold, the TRPC4 structure deviates from other TRP channels with a unique cytosolic domain. This unique cytosolic N-terminal domain forms extensive aromatic contacts with the TRP and the C-terminal domains. The comparison of our structure with other known TRP structures provides molecular insights into TRPC4 ion selectivity and extends our knowledge of the diversity and evolution of the TRP channels.
History
DepositionFeb 2, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

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Assembly

Deposited unit
A: Short transient receptor potential channel 4
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)354,90317
Polymers350,2464
Non-polymers4,65713
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area46780 Å2
ΔGint-374 kcal/mol
Surface area116720 Å2

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Components

#1: Protein
Short transient receptor potential channel 4 / TrpC4 / Capacitative calcium entry channel Trp4 / Receptor-activated cation channel TRP4


Mass: 87561.516 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Trpc4, Trrp4 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9QUQ5
#2: Chemical
ChemComp-Y01 / CHOLESTEROL HEMISUCCINATE


Mass: 486.726 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C31H50O4
#3: 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
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na

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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 TRPC4 / 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 FIELDBright-field microscopy
Image recordingElectron dose: 56 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 232858 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00821821
ELECTRON MICROSCOPYf_angle_d1.15429639
ELECTRON MICROSCOPYf_dihedral_angle_d12.12613163
ELECTRON MICROSCOPYf_chiral_restr0.0613397
ELECTRON MICROSCOPYf_plane_restr0.0073685

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