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- EMDB-65735: Cryo-EM structure of dPIEZO channel -

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Basic information

Entry
Database: EMDB / ID: EMD-65735
TitleCryo-EM structure of dPIEZO channel
Map datadPiezo combined map
Sample
  • Complex: dPIEZO Structure
    • Protein or peptide: Piezo-type mechanosensitive ion channel component
  • Ligand: (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
  • Ligand: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
  • Ligand: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
KeywordsdPIEZO channel / MEMBRANE PROTEIN
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
Piezo-type mechanosensitive ion channel component
Similarity search - Component
Biological speciesDrosophila (fruit flies)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.95 Å
AuthorsLiu S / Li X / Xiao B
Funding support China, 5 items
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, 2025-
Header (metadata) releaseMay 6, 2026-
Map releaseMay 6, 2026-
UpdateMay 6, 2026-
Current statusMay 6, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65735.png

Downloads & links

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Map

FileDownload / File: emd_65735.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationdPiezo combined map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.33 Å/pix.
x 300 pix.
= 399. Å		1.33 Å/pix.
x 300 pix.
= 399. Å		1.33 Å/pix.
x 300 pix.
= 399. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.33 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.35
Minimum - Maximum-1.4617674 - 4.0176706
Average (Standard dev.)0.021894475 (±0.08366904)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 399.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: dPIEZO halfB map

Fileemd_65735_half_map_1.map
AnnotationdPIEZO halfB map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: dPIEZO halfA map

Fileemd_65735_half_map_2.map
AnnotationdPIEZO halfA map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : dPIEZO Structure

EntireName: dPIEZO Structure
Components
  • Complex: dPIEZO Structure
    • Protein or peptide: Piezo-type mechanosensitive ion channel component
  • Ligand: (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
  • Ligand: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
  • Ligand: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine

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Supramolecule #1: dPIEZO Structure

SupramoleculeName: dPIEZO Structure / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Drosophila (fruit flies)

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Macromolecule #1: Piezo-type mechanosensitive ion channel component

MacromoleculeName: Piezo-type mechanosensitive ion channel component / type: protein_or_peptide / ID: 1
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
Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Drosophila (fruit flies)
Molecular weightTheoretical: 289.74625 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MVFSYACMVL QRIVVPAVLV LAALMRPVGI SFVYLLMFFV SPFVPLATRR NFKGSVTAFF IILLTLSTLV LLGHITLQIL AVSLTLPIY NCSFSERLLR HIGFVSFIDL QPFAIIEWLV PEVLVFATSL GSYLTVKRVA SQPVGAEQLE NGEVVDGQAE N AQTSSQPS ...String:
MVFSYACMVL QRIVVPAVLV LAALMRPVGI SFVYLLMFFV SPFVPLATRR NFKGSVTAFF IILLTLSTLV LLGHITLQIL AVSLTLPIY NCSFSERLLR HIGFVSFIDL QPFAIIEWLV PEVLVFATSL GSYLTVKRVA SQPVGAEQLE NGEVVDGQAE N AQTSSQPS AADANGGDVQ QATVTTPLQQ QQQQLRKRVS MISQHIHFEG LVKISPLFCL ATLFFAAVLR PSVPGGFYFL IF LLSGTYW ATCQTLQRGF ALLLRCVMVV LVLHSLSIVS YQTPWMQSHL NHTTLTARLI GLEPLIESYC SPDIRVFLYN NKL SLDSYL NPFALFFAYF ALALTTKHLI KPRLVRQSTR KARTPQPLES GSSVAPSVTQ RGNDMQLESM EQRSEQENTT TSIL DQISY GFVSVGGFIY QNSYIFTNIL MMAWSIVYHS WLTFVLLLSA NVLWMIPNQR KAMMRSSPFI VLYAEALLIA QYIYG MDLN NEELPTSVPT AGINLQQIGF ERPIENQMRP CVPLIVKTAF VLMFWVTSRQ FFKEKRDRRR DSTLADFIAP LQITVG SAG SSYLINDGKK TSKFLKKAGD VIKNLLVRLW IWLLVLVIFL CAITGENMTG FRICYMALFL FFLLVFQSSS KAWVKIM YG FWLFLIFYAM SILILIYTYQ FDKFDTYWSD YLNVSATLQK DIGLKRYQTK DLFLHLVSPT IIVILTVIQV HYFHKRFI A SLQQQPLAGG SAQQKPTETT ALEPAPSKRR GSAGSLRKSQ GPSAEAAPGA TTDFETSVRD LVRISFRKIK NKSEYIFKN FKDVFWRFLE LHIMKAVYIA AFVCSVSEVC VLHIIFVGFC VLGATSRKAV QVVISRLISF IVTVIVLSKM IYQIEYLSHS QHNVVCSDN RTANNAEWIG LTKADKVTGG LMSLLRTYII YMVIVTMHAV ISLRQLQMRV KIGALNAPPT KLLFPNIIRA D AEKDLVGL VKYLLNFGFY KFGIEISLIA LVSTITYRQD IVAVVYALWL VVLLLLRRSQ CAKIWGVFQA FFAISILTQY IV LVGLPPS SCLVFPWDEG PFGEGIQRWA MLPGALHFNH VPKLIFDFIV LVILNRQKSI FCIEQRYASN DDYPGGSNRS VIA DIAQLG RVPFDNPTHD FCSYIRNYSD ILKNGVLCGF YWFTLAVVFL AGTNIADLLA LGYLIGAFIF LWQGSDFYLR PIHT IIFRW KWLLAFNVAN ILIKTSFQMA GCLFMTQLTK DCCWLVHMLG ITCTSNVLTE QIMLPEEAEL ALKPGECPKI THQVV LLWD TICFAFIIFQ LRIFKSHYFC HIITDTKANN ILASRGADII ESLRHKQIAH RHDHEKQVLH KIKRKMERIR ATQQKM LRP LDKQTHFDEH GYPLPAPTVR RRKEIKLHPH ATRAGDYYMF EEMDDKFELD LIHDEIDFLE EENITESEMK MQRRKTL YD KSKDAPTGEF PSTSKGISKE RDAATASSSA SPAPTRDVGD LPVIPPPSTG LGREQTSKET SDSKSKMEVD SGEVTAKD S DEDFDTNPII RLLEGFLVTL TIRLNRFSRN YRFVNRILAG EKKTLKESSS LNRLGLSSAA AMFHFLKSNL ESDESEPPA SSSTPRRVVI APPNATEHSD PTSTTLNTNT TTTPLSPPEP LQPLQPLQPN TTSTPQQQHQ HIRAAEEIIE LPVDTVDGVA HRKQSINSS PPAKGAGEFN LEEENFAQRD HHIIVEVLIS SWYALLANTD LICYIVVFIN QVVNASLISL PLPIMVFLWG T LSLPRPTK TFWVTLIAYT QAIVLIKCIF QFKLIWSNYH QLPNQPLTPA KIFGVENKAH YAIYDLILLL VLFLHRYLLK SQ GLWKSGY KDTDNQFTKP TASIDERDDS DNLSQPDSRQ LNDDAAQKLS LQVSQASLPG SPEFSKTGIN QLERTKYTSS LYK FFFSLV HKSRLATDVY ALMFLCDFVN FFVLLFGFTA FGTQQTESDE GVQTYLAENK VPIPFLIMLL VQFLLIVIDR ALYL RKALV NKIIFHFFSV IGIHIWMFFV VPAVTERTFN SLAPPIIFYV IKCFYMLLSS YQIKSGYPKR ILGNFFTKGF SMVNM IAFK VYMQIPFLYE LRTILDWVCI DSTMTIFDWL KMEDIFSNIY LIRCTRQSET DFPAMRAQKK ASLSKLIMGG TIVLLI VIC IWGPLCLFAL GNAVGTSNVP FHVSLSIRIG PYDPIYTTNN YDSIFEINPE MYSQMTNAYI KEKQALTFIA GYDATDV AA VRLAGNSPSL WNIAPPDRQR LLNDLRNNHT LKARFSYSLT RKAPAKGLKE NVGDEHAISL DESFEGRAAL IHMLSETH D VEPIYSNGTT NGTTPEVEEV VVIPGMIPKF IKVLNSGDAA VVSVLSPKHY DYRPLVIKMH RDNETNGLWW EIRDYCNDT FYNETLSKFA YSNCTSGIVM YTFNDKKFPS TFSFLTAGGI IGLYTTFVLL ASRFMKSFIG GQNRKIMFED LPYVDRVLQL CLDIYLVRE ALEFALEEDL FAKLLFLYRS PETLIKWTRP KEEYVDDDGD TDSIPSRMSV RRPEQLQPQQ PQ

UniProtKB: Piezo-type mechanosensitive ion channel component

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Macromolecule #2: (9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,...

MacromoleculeName: (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
type: ligand / ID: 2 / Number of copies: 12 / Formula: PLX
Molecular weightTheoretical: 767.132 Da
Chemical component information

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 / phospholipid*YM

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Macromolecule #3: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine

MacromoleculeName: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / type: ligand / ID: 3 / Number of copies: 3 / Formula: PEE
Molecular weightTheoretical: 744.034 Da
Chemical component information

ChemComp-PEE:
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE, phospholipid*YM

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Macromolecule #4: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phospho...

MacromoleculeName: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
type: ligand / ID: 4 / Number of copies: 3 / Formula: P5S
Molecular weightTheoretical: 792.075 Da
Chemical component information

ChemComp-P5S:
O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.3
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.95 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 678118
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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