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- PDB-5z10: Structure of the mechanosensitive Piezo1 channel -

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Basic information

Entry
Database: PDB / ID: 5z10
TitleStructure of the mechanosensitive Piezo1 channel
ComponentsPiezo-type mechanosensitive ion channel component 1
KeywordsMEMBRANE PROTEIN / Piezo1 / Piezo2 / mechanogating / channel
Function / homology
Function and homology information


mechanosensitive monoatomic cation channel activity / positive regulation of cell-cell adhesion mediated by integrin / detection of mechanical stimulus / mechanosensitive monoatomic ion channel activity / positive regulation of integrin activation / positive regulation of myotube differentiation / lamellipodium membrane / monoatomic cation transport / monoatomic cation channel activity / regulation of membrane potential ...mechanosensitive monoatomic cation channel activity / positive regulation of cell-cell adhesion mediated by integrin / detection of mechanical stimulus / mechanosensitive monoatomic ion channel activity / positive regulation of integrin activation / positive regulation of myotube differentiation / lamellipodium membrane / monoatomic cation transport / monoatomic cation channel activity / regulation of membrane potential / endoplasmic reticulum-Golgi intermediate compartment membrane / cellular response to mechanical stimulus / endoplasmic reticulum membrane / endoplasmic reticulum / identical protein binding / plasma membrane
Similarity search - Function
Piezo family / Piezo non-specific cation channel, R-Ras-binding domain / Piezo domain / Piezo non-specific cation channel, R-Ras-binding domain / Piezo
Similarity search - Domain/homology
Piezo-type mechanosensitive ion channel component 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.97 Å
AuthorsZhao, Q. / Zhou, H. / Chi, S. / Wang, Y. / Wang, J. / Geng, J. / Wu, K. / Liu, W. / Zhang, T. / Dong, M.-Q. ...Zhao, Q. / Zhou, H. / Chi, S. / Wang, Y. / Wang, J. / Geng, J. / Wu, K. / Liu, W. / Zhang, T. / Dong, M.-Q. / Wang, J. / Li, X. / Xiao, B.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31630090 China
CitationJournal: Nature / Year: 2018
Title: Structure and mechanogating mechanism of the Piezo1 channel.
Authors: Qiancheng Zhao / Heng Zhou / Shaopeng Chi / Yanfeng Wang / Jianhua Wang / Jie Geng / Kun Wu / Wenhao Liu / Tingxin Zhang / Meng-Qiu Dong / Jiawei Wang / Xueming Li / Bailong Xiao /
Abstract: The mechanosensitive Piezo channels function as key eukaryotic mechanotransducers. However, their structures and mechanogating mechanisms remain unknown. Here we determine the three-bladed, propeller- ...The mechanosensitive Piezo channels function as key eukaryotic mechanotransducers. However, their structures and mechanogating mechanisms remain unknown. Here we determine the three-bladed, propeller-like electron cryo-microscopy structure of mouse Piezo1 and functionally reveal its mechanotransduction components. Despite the lack of sequence repetition, we identify nine repetitive units consisting of four transmembrane helices each-which we term transmembrane helical units (THUs)-which assemble into a highly curved blade-like structure. The last transmembrane helix encloses a hydrophobic pore, followed by three intracellular fenestration sites and side portals that contain pore-property-determining residues. The central region forms a 90 Å-long intracellular beam-like structure, which undergoes a lever-like motion to connect THUs to the pore via the interfaces of the C-terminal domain, the anchor-resembling domain and the outer helix. Deleting extracellular loops in the distal THUs or mutating single residues in the beam impairs the mechanical activation of Piezo1. Overall, Piezo1 possesses a unique 38-transmembrane-helix topology and designated mechanotransduction components, which enable a lever-like mechanogating mechanism.
History
DepositionDec 22, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.2Mar 7, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 2.0Jan 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations / Refinement description / Structure summary
Category: atom_site / computing ...atom_site / computing / em_software / pdbx_audit_support / pdbx_poly_seq_scheme / pdbx_struct_assembly_prop / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_torsion / refine_ls_restr / software / struct_conf / struct_conn / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _em_software.category / _pdbx_poly_seq_scheme.auth_mon_id ..._em_software.category / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _software.version / _struct_conn.pdbx_dist_value
Description: Model completeness / Provider: author / Type: Coordinate replacement

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Structure visualization

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Assembly

Deposited unit
A: Piezo-type mechanosensitive ion channel component 1
B: Piezo-type mechanosensitive ion channel component 1
C: Piezo-type mechanosensitive ion channel component 1


Theoretical massNumber of molelcules
Total (without water)876,9623
Polymers876,9623
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Piezo-type mechanosensitive ion channel component 1 / Protein FAM38A


Mass: 292320.656 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Piezo1, Fam38a / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: E2JF22

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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 map of the mechanosensitive Piezo1 channel / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293T
Buffer solutionpH: 7.2
SpecimenConc.: 0.18 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K
Details: After a 15 sec waiting time, the grids were blotted for 3.5 sec and plunged into liquid ethane

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 22500 X / Nominal defocus min: 1500 nm / Calibrated defocus min: 3000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 8 sec. / Electron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 32 / Used frames/image: 1-32

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Processing

SoftwareName: PHENIX / Version: dev_3374: / Classification: refinement
EM software
IDNameVersionCategory
2UCSFImage4image acquisition
4RELION1.4CTF correction
10RELION1.4initial Euler assignment
11RELION1.4final Euler assignment
12RELION1.4classification
13RELION1.43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 3.97 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 238529 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00629763
ELECTRON MICROSCOPYf_angle_d1.02940506
ELECTRON MICROSCOPYf_dihedral_angle_d10.10717556
ELECTRON MICROSCOPYf_chiral_restr0.0594716
ELECTRON MICROSCOPYf_plane_restr0.0085148

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