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- PDB-6b3r: Structure of the mechanosensitive channel Piezo1 -

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Basic information

Entry
Database: PDB / ID: 6b3r
TitleStructure of the mechanosensitive channel Piezo1
Components
  • Piezo-type mechanosensitive ion channel component 1
  • Piezo-type mechanosensitive ion channel component 1, unknown fragment
KeywordsTRANSPORT PROTEIN / triskelion / transmembrane / ion channel / MEMBRANE PROTEIN
Function / homology
Function and homology information


mechanosensitive monoatomic cation channel activity / cuticular plate / positive regulation of cell-cell adhesion mediated by integrin / detection of mechanical stimulus / positive regulation of integrin activation / mechanosensitive monoatomic ion channel activity / stereocilium / positive regulation of myotube differentiation / lamellipodium membrane / monoatomic cation transport ...mechanosensitive monoatomic cation channel activity / cuticular plate / positive regulation of cell-cell adhesion mediated by integrin / detection of mechanical stimulus / positive regulation of integrin activation / mechanosensitive monoatomic ion channel activity / stereocilium / positive regulation of myotube differentiation / lamellipodium membrane / monoatomic cation transport / monoatomic cation channel activity / endoplasmic reticulum-Golgi intermediate compartment membrane / regulation of membrane potential / 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, cap domain / Piezo TM25-28
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
AuthorsGuo, Y.R. / MacKinnon, R.
CitationJournal: Elife / Year: 2017
Title: Structure-based membrane dome mechanism for Piezo mechanosensitivity.
Authors: Yusong R Guo / Roderick MacKinnon /
Abstract: Mechanosensitive ion channels convert external mechanical stimuli into electrochemical signals for critical processes including touch sensation, balance, and cardiovascular regulation. The best ...Mechanosensitive ion channels convert external mechanical stimuli into electrochemical signals for critical processes including touch sensation, balance, and cardiovascular regulation. The best understood mechanosensitive channel, MscL, opens a wide pore, which accounts for mechanosensitive gating due to in-plane area expansion. Eukaryotic Piezo channels have a narrow pore and therefore must capture mechanical forces to control gating in another way. We present a cryo-EM structure of mouse Piezo1 in a closed conformation at 3.7Å-resolution. The channel is a triskelion with arms consisting of repeated arrays of 4-TM structural units surrounding a pore. Its shape deforms the membrane locally into a dome. We present a hypothesis in which the membrane deformation changes upon channel opening. Quantitatively, membrane tension will alter gating energetics in proportion to the change in projected area under the dome. This mechanism can account for highly sensitive mechanical gating in the setting of a narrow, cation-selective pore.
History
DepositionSep 22, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1May 16, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / em_admin / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update

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Assembly

Deposited unit
A: Piezo-type mechanosensitive ion channel component 1
B: Piezo-type mechanosensitive ion channel component 1, unknown fragment
C: Piezo-type mechanosensitive ion channel component 1
E: Piezo-type mechanosensitive ion channel component 1
D: Piezo-type mechanosensitive ion channel component 1, unknown fragment
F: Piezo-type mechanosensitive ion channel component 1, unknown fragment


Theoretical massNumber of molelcules
Total (without water)881,1016
Polymers881,1016
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area22990 Å2
ΔGint-132 kcal/mol
Surface area237020 Å2

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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 / Plasmid: pEG BacMam / Cell line (production host): HEK293S GnTI- / Production host: Homo sapiens (human) / References: UniProt: E2JF22
#2: Protein/peptide Piezo-type mechanosensitive ion channel component 1, unknown fragment


Mass: 1379.692 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Piezo1 / Plasmid: pEG BacMam / Cell line (production host): HEK293S GnTl- / Production host: Homo sapiens (human)
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 Piezo1 channel / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.9 MDa / Experimental value: NO
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Homo sapiens (human) / Strain: HEK293S GnTl- / Plasmid: pEG BacMam
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTrisTris1
2150 mMsodium chlorideNaCl1
30.05 % w/vdigitonin1
SpecimenConc.: 15 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse
Specimen supportGrid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K / Details: blot for 1 second with -1 force before plunging

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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 FIELD
Image recordingAverage exposure time: 10 sec. / Electron dose: 47 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3414
Image scansMovie frames/image: 50 / Used frames/image: 1-50

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Processing

SoftwareName: PHENIX / Version: 1.12_2829: / Classification: refinement
EM software
IDNameVersionCategory
1RELION1.4particle selection
2SerialEMimage acquisition
4RELION2CTF correction
7Coot0.8.7model fitting
9cryoSPARCinitial Euler assignment
10RELION2final Euler assignment
11RELION2classification
12RELION23D reconstruction
13PHENIX1.12-2829model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 576191
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 277548 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL / Target criteria: correlation coefficient
Atomic model buildingPDB-ID: 4RAX

4rax


Accession code: 4RAX / Pdb chain residue range: 2214-2457 / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00636603
ELECTRON MICROSCOPYf_angle_d1.03249776
ELECTRON MICROSCOPYf_dihedral_angle_d7.92921675
ELECTRON MICROSCOPYf_chiral_restr0.0575679
ELECTRON MICROSCOPYf_plane_restr0.0076246

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