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- PDB-6bpz: Structure of the mechanically activated ion channel Piezo1 -

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Basic information

Entry
Database: PDB / ID: 6bpz
TitleStructure of the mechanically activated ion channel Piezo1
ComponentsPiezo-type mechanosensitive ion channel component 1,Piezo-type mechanosensitive ion channel component 1,mouse Piezo1,Piezo-type mechanosensitive ion channel component 1,Piezo-type mechanosensitive ion channel component 1
KeywordsMEMBRANE PROTEIN / mechanosensitive ion 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: 3.8 Å
AuthorsSaotome, K. / Kefauver, J.M. / Patapoutian, A. / Ward, A.B.
Funding support United States, 4items
OrganizationGrant numberCountry
Ray Thomas Edwards Foundation United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS083174 United States
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)DE022358 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nature / Year: 2018
Title: Structure of the mechanically activated ion channel Piezo1.
Authors: Kei Saotome / Swetha E Murthy / Jennifer M Kefauver / Tess Whitwam / Ardem Patapoutian / Andrew B Ward /
Abstract: Piezo1 and Piezo2 are mechanically activated ion channels that mediate touch perception, proprioception and vascular development. Piezo proteins are distinct from other ion channels and their ...Piezo1 and Piezo2 are mechanically activated ion channels that mediate touch perception, proprioception and vascular development. Piezo proteins are distinct from other ion channels and their structure remains poorly defined, which impedes detailed study of their gating and ion permeation properties. Here we report a high-resolution cryo-electron microscopy structure of the mouse Piezo1 trimer. The detergent-solubilized complex adopts a three-bladed propeller shape with a curved transmembrane region containing at least 26 transmembrane helices per protomer. The flexible propeller blades can adopt distinct conformations, and consist of a series of four-transmembrane helical bundles that we term Piezo repeats. Carboxy-terminal domains line the central ion pore, and the channel is closed by constrictions in the cytosol. A kinked helical beam and anchor domain link the Piezo repeats to the pore, and are poised to control gating allosterically. The structure provides a foundation to dissect further how Piezo channels are regulated by mechanical force.
History
DepositionNov 27, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 3, 2018Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 7, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Jul 18, 2018Group: Data collection / Experimental preparation / Category: em_sample_support / Item: _em_sample_support.grid_type
Revision 1.4Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 18, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]

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Assembly

Deposited unit
A: Piezo-type mechanosensitive ion channel component 1,Piezo-type mechanosensitive ion channel component 1,mouse Piezo1,Piezo-type mechanosensitive ion channel component 1,Piezo-type mechanosensitive ion channel component 1
B: Piezo-type mechanosensitive ion channel component 1,Piezo-type mechanosensitive ion channel component 1,mouse Piezo1,Piezo-type mechanosensitive ion channel component 1,Piezo-type mechanosensitive ion channel component 1
C: Piezo-type mechanosensitive ion channel component 1,Piezo-type mechanosensitive ion channel component 1,mouse Piezo1,Piezo-type mechanosensitive ion channel component 1,Piezo-type mechanosensitive ion channel component 1


Theoretical massNumber of molelcules
Total (without water)485,9213
Polymers485,9213
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,Piezo-type mechanosensitive ion channel component 1,mouse Piezo1,Piezo-type mechanosensitive ion channel component 1,Piezo-type mechanosensitive ion channel component 1 / Protein FAM38A


Mass: 161973.531 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Piezo1, Fam38a / 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: mouse Piezo1 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.876 MDa / Experimental value: NO
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293F
Buffer solutionpH: 8
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: mouse Piezo1 was purified in glyco-diosgenin.
Specimen supportGrid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil, UltrAuFoil
VitrificationCryogen name: 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
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
EM software
IDNameVersionCategory
1RELION2particle selection
2Leginonimage acquisition
4Gctf0.5CTF correction
7Cootmodel fitting
9RELION2initial Euler assignment
10RELION2final Euler assignment
12RELION3D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 72627 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01222041
ELECTRON MICROSCOPYf_angle_d1.5629910
ELECTRON MICROSCOPYf_dihedral_angle_d12.76713020
ELECTRON MICROSCOPYf_chiral_restr0.0773450
ELECTRON MICROSCOPYf_plane_restr0.016348

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