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- PDB-8ixn: Curved structure of mPIEZO1-S2472E -

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Basic information

Entry
Database: PDB / ID: 8ixn
TitleCurved structure of mPIEZO1-S2472E
ComponentsPiezo-type mechanosensitive ion channel component 1
KeywordsMEMBRANE PROTEIN / Closed-state structure / PIEZO1 channel
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 / monoatomic cation transport / lamellipodium membrane ...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 / monoatomic cation transport / lamellipodium membrane / 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, R-Ras-binding domain / Piezo
Similarity search - Domain/homology
Chem-P5S / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / Chem-PLX / Piezo-type mechanosensitive ion channel component 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.07 Å
AuthorsLiu, S. / Yang, X. / Chen, X. / Li, X. / Xiao, B.
Funding support China, 5items
OrganizationGrant numberCountry
Other government2016YFA0500402
National Natural Science Foundation of China (NSFC)31825014 China
National Natural Science Foundation of China (NSFC)32130049 China
National Natural Science Foundation of China (NSFC)32021002 China
National Natural Science Foundation of China (NSFC)31630090 China
CitationJournal: Neuron / Year: 2024
Title: An intermediate open structure reveals the gating transition of the mechanically activated PIEZO1 channel.
Authors: Sijia Liu / Xuzhong Yang / Xudong Chen / Xiaochun Zhang / Jinghui Jiang / Jingyi Yuan / Wenhao Liu / Li Wang / Heng Zhou / Kun Wu / Boxue Tian / Xueming Li / Bailong Xiao /
Abstract: PIEZO1 is a mechanically activated cation channel that undergoes force-induced activation and inactivation. However, its distinct structural states remain undefined. Here, we employed an open-prone ...PIEZO1 is a mechanically activated cation channel that undergoes force-induced activation and inactivation. However, its distinct structural states remain undefined. Here, we employed an open-prone PIEZO1-S2472E mutant to capture an intermediate open structure. Compared with the curved and flattened structures of PIEZO1, the S2472E-Intermediate structure displays partially flattened blades, a downward and rotational motion of the top cap, and a spring-like compression of the linker connecting the cap to the pore-lining inner helix. These conformational changes open the cap gate and the hydrophobic transmembrane gate, whereas the intracellular lateral plug gate remains closed. The flattened structure of PIEZO1 with an up-state cap and closed cap gate might represent an inactivated state. Molecular dynamics (MD) simulations of ion conduction support the closed, intermediate open, and inactivated structural states. Mutagenesis and electrophysiological studies identified key domains and residues critical for the mechanical activation of PIEZO1. These studies collectively define the distinct structural states and gating transitions of PIEZO1.
History
DepositionApr 1, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 1, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Piezo-type mechanosensitive ion channel component 1
A: Piezo-type mechanosensitive ion channel component 1
D: Piezo-type mechanosensitive ion channel component 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)886,29915
Polymers877,0883
Non-polymers9,21112
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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


Mass: 292362.688 Da / Num. of mol.: 3 / Mutation: S2472E
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
#2: Chemical
ChemComp-PLX / (9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,7,10-TRIOXA-2LAMBDA~5~-AZA-6LAMBDA~5~-PHOSPHAOCTACOSANE-6,6,11-TRIOL


Mass: 767.132 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C42H89NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#3: Chemical ChemComp-PEE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE


Mass: 744.034 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C41H78NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: DOPE, phospholipid*YM
#4: Chemical ChemComp-P5S / O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine / phosphatidyl serine


Mass: 792.075 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C42H82NO10P / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: S2472E-Curved Structure / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.3
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: 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 / Nominal defocus max: 2300 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 4.07 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 488709 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00430123
ELECTRON MICROSCOPYf_angle_d0.79541073
ELECTRON MICROSCOPYf_dihedral_angle_d4.5794275
ELECTRON MICROSCOPYf_chiral_restr0.0464941
ELECTRON MICROSCOPYf_plane_restr0.0065205

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