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- PDB-9w7x: Cryo-EM structure of dPIEZO channel -

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Basic information

Entry
Database: PDB / ID: 9w7x
TitleCryo-EM structure of dPIEZO channel
ComponentsPiezo-type mechanosensitive ion channel component
KeywordsMEMBRANE PROTEIN / dPIEZO channel
Function / homology
Function and homology information


mechanosensory behavior / detection of mechanical stimulus / mechanosensitive monoatomic ion channel activity / detection of temperature stimulus involved in sensory perception of pain / monoatomic cation transmembrane transport / monoatomic cation channel activity / cellular response to mechanical stimulus / regulation of membrane potential / monoatomic ion transmembrane transport / 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 / Piezo1-like, transmembrane helical unit / Piezo TM1-24 / Piezo, THU9 and anchor domain
Similarity search - Domain/homology
Chem-P5S / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / Chem-PLX / Piezo-type mechanosensitive ion channel component
Similarity search - Component
Biological speciesDrosophila (fruit flies)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.95 Å
AuthorsLiu, S. / Li, X. / Xiao, B.
Funding support China, 5items
OrganizationGrant numberCountry
Other government2016YFA0500402 China
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: To Be Published
Title: Cryo-EM structure of dPIEZO channel
Authors: Liu, S. / Yang, X. / Chen, X. / Li, X. / Xiao, B.
History
DepositionAug 7, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 6, 2026Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

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MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)883,05321
Polymers869,2393
Non-polymers13,81418
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Piezo-type mechanosensitive ion channel component


Mass: 289746.250 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: Sequence reference for Drosophila is not available at the time of biocuration. Current sequence reference is from UniProt id M9MSG8.Residue 2323 is HIS in our construct, consistent with the ...Details: Sequence reference for Drosophila is not available at the time of biocuration. Current sequence reference is from UniProt id M9MSG8.Residue 2323 is HIS in our construct, consistent with the experimentally determined sequence. The UniProt entry M9MSG8 appears to have a TYR at this position, likely representing a different isoform or annotation error
Source: (gene. exp.) Drosophila (fruit flies) / Gene: Piezo, CG18103 / Production host: Homo sapiens (human) / References: UniProt: M9MSG8
#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.: 12 / 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: dPIEZO Structure / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Drosophila (fruit flies)
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: TFS 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

EM software
IDNameVersionCategory
1RELION3.1particle selection
8PHENIXmodel refinement
13RELION3.13D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.95 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 678118 / Symmetry type: POINT
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00331770
ELECTRON MICROSCOPYf_angle_d0.61543104
ELECTRON MICROSCOPYf_dihedral_angle_d3.5314197
ELECTRON MICROSCOPYf_chiral_restr0.0415028
ELECTRON MICROSCOPYf_plane_restr0.0045277

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