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- EMDB-64385: Structure of C. elegans piezo channel -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-64385
TitleStructure of C. elegans piezo channel
Map data
Sample
  • Complex: C. elegans Piezo channel
    • Protein or peptide: Piezo-type mechanosensitive ion channel component 1
Keywordsmechanosensitive channel / MEMBRANE PROTEIN
Function / homology
Function and homology information


positive regulation of brood size / positive regulation of ovulation / detection of mechanical stimulus / flagellated sperm motility / mechanosensitive monoatomic ion channel activity / monoatomic cation transmembrane transport / response to mechanical stimulus / monoatomic cation channel activity / regulation of membrane potential / cellular response to mechanical stimulus / 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 1
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsLiu Y / Guo YR
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Cell Rep / Year: 2025
Title: Membrane dome-based regulation mechanism of the mechanosensitive PIEZO channel.
Authors: Yushuang Liu / Bowen Liu / Weiran Zhan / Lun Zhang / Anbing Shi / Long Lin / Man Jiang / Yusong R Guo /
Abstract: PIEZO channels are mechanosensitive ion channels essential for various physiological processes. How activation of PIEZO channels is regulated for distinct mechanical environments remains largely ...PIEZO channels are mechanosensitive ion channels essential for various physiological processes. How activation of PIEZO channels is regulated for distinct mechanical environments remains largely unclear. Here, we use patch-clamp electrophysiology to record pressure-activated currents of natural splicing isoforms of Caenorhabditis elegans PIEZO channels that differ in sequence length. These isoforms are sensitive in different tension regimes, consistent with the quantitative prediction from the membrane dome mechanism, based on structural measurement from cryo-electron microscopy data. Furthermore, these isoforms show different localization in the worm body and are involved in different physiological functions. Therefore, inspired by the membrane dome mechanism, a distinct regulatory strategy is found for PIEZO channels to tune the mechanosensitivity by adjusting the dome area via alternative splicing to adapt to the physiological environment.
History
DepositionApr 27, 2025-
Header (metadata) releaseDec 24, 2025-
Map releaseDec 24, 2025-
UpdateDec 24, 2025-
Current statusDec 24, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64385.png

Downloads & links

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Map

FileDownload / File: emd_64385.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 560 pix.
= 532. Å		0.95 Å/pix.
x 560 pix.
= 532. Å		0.95 Å/pix.
x 560 pix.
= 532. Å

Surface

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Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.075
Minimum - Maximum-0.1404821 - 0.40091273
Average (Standard dev.)-0.000092268696 (±0.009174447)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions560560560
Spacing560560560
CellA=B=C: 532.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: sharpened

Fileemd_64385_additional_1.map
Annotationsharpened
Projections & Slices
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Slices (1/2)
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Half map: #2

Fileemd_64385_half_map_1.map
Projections & Slices
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Histogram

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Half map: #1

Fileemd_64385_half_map_2.map
Projections & Slices
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Sample components

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Entire : C. elegans Piezo channel

EntireName: C. elegans Piezo channel
Components
  • Complex: C. elegans Piezo channel
    • Protein or peptide: Piezo-type mechanosensitive ion channel component 1

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Supramolecule #1: C. elegans Piezo channel

SupramoleculeName: C. elegans Piezo channel / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Caenorhabditis elegans (invertebrata)

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Macromolecule #1: Piezo-type mechanosensitive ion channel component 1

MacromoleculeName: Piezo-type mechanosensitive ion channel component 1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 277.068031 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MTVPPLLKSC VVKLLLPAAL LAAAIIRPSF LSIGYVLLAL VSAVLPPIRK SLALPKLVGT FVIITFLFCL AVALGVGSYQ ISEQVVHKN DRTYICNRSD TTLFRSIGLV RFHPTGTFES TRAFLPEIIA TSAALLTIII VMFLSHRDEQ LDVVGDVVTV R SESGREQR ...String:
MTVPPLLKSC VVKLLLPAAL LAAAIIRPSF LSIGYVLLAL VSAVLPPIRK SLALPKLVGT FVIITFLFCL AVALGVGSYQ ISEQVVHKN DRTYICNRSD TTLFRSIGLV RFHPTGTFES TRAFLPEIIA TSAALLTIII VMFLSHRDEQ LDVVGDVVTV R SESGREQR RQRKLAAIMW SAIGNSLRRL TNFVLFLFTA YVGIVKPSLS NSIYFLAFLF ISTWWSTYTP LRHGVYNQIK KF LIFYSAL HFLVLYTYQI PIVHHSWLPT GSFLPRLFGL TVLMDSSCPE WWKFPFVAPD FNDDDLIMKW PLYANPIVVL VFF YLTVAQ YKFTRNGSRE YIDDNEYGSS VHEERFVSAG TVETNVDDVG QLISISESTA SAPSGRGRGN TLLLSNASSS ANDD EQGRA RSRSPLRNGE EQGSIPLRKV TSQVVDRNKL SNIFNTTAPG DKESAASKGM IAVMTFVIFH SYSIALTAMM TWALL YHSI FGLILLILTC ILWIFRDTRK SSFAMAPIIL MYIEFLLILQ YFLSMDIHAE IGDPAWMNFV GIEWTTLPVH AVIILC VQT LLTLPVFLLL RLARREKFYE SLSDYERQRR INSYGTFGAS KTGAGGVAVA KFQDPKSRKF AAFVEYLSNK VSVYFIF VV SVVLLVVSTC FAPNFYNILF FALWALNLIY LKFSFRLYRG LAYAFWLTLT FYTSIVIIAL YIYQFPGVSQ WIIRNTSL S QEWLNAIGLV DFRAIGESGA LFLQLLAPIA LFVVTMLQLK FFHGPWSRAT SPRRAENDPP TSTTEAAAVA STSGTQGRA HAAGDTLVKK LHKLANQTIE LLWRFFEVHI SKIVFVIIAI FIANNINALY IPLVILLSLA ICLPSAADGI FSLFMCAYLF LVALSKMIY QLDIVPELSQ IDRGVGADNC SHGNISMPEW FGLKKEVEGT EPIYMLFGVI VSIIALAFQS IVIYRQRHYR A SLGLPESM RAKVFPDFHH SHFDRSLKNA IQFLIDYGFY KFGLEITMIA IGIDIFNRMD ALAAIQCFWL VLFALNKRVF VR RIWVFYV IYMAILYPLQ FFSYVGLPPD SCIEYPWSYW IPSYSDDARF NLSYLLNLSI YGVNWPSAYL IGDFFVLLLA SCQ LAVFRR EGEDNDSIYN DGNFVIKPEN PQYDFIDTKK SYVDYFKSFV FHYGHWITLM STLAAGIAGT SLFALGYIIF TLTM LWSGN NLYVMNSTLR SFEHTLKRWN ALLGYTLFTI TMKVCLQIFG CVFLSWFDQS GGWGKTLCIV RQLFSITCVN NECHV LKEL EDFSKACAVE TKEGNIGFDV IALSFLVFQI RIFHSWYFQH CMVEYRSEVI LANRGAVLKN QLIEKEMKEQ NEQQKA KFN DIRRRTEAIR ERYQKQIERG AAERDFEPVT YGHAKRAGDY YMFKYDPEND DLVEPVDSFV PEVDPKATAY DRLDPGQ IM YAATAHDLDL AKTVQQVKKG DTIKDPDSRA LIAVSEPEAR KPGGTEETDG DEDEDNKDSK VESTAKFIQK MIASALDL C SVTLNKLCRE HRYVGFVLSK EKQKLKSGHS ESLSNTSRKL TDIRSAVDLP SLQLVQSAND VEKMETAVSV DWQQKSSAT RLLNAVVNCI GAHTDILCYF FAIMTQVMTG GLITLPLPLM SLFWGNLSNP RPSKFFWVTM ITYTECVIVI KFVCQFAFMP YNSITWRTE HQMDPMSLDK LFGVSQRDSF ALWDIVLLFS LFFHRYMLRK LGLWKDANLT DTFTLKEEPR SASGSDTGSP K KIAQEPKV VVTQSDTLEG TSGGEIVIPS DPNAVSNMEE LDCEPPIPEK QSGPIGRFIH QLFHPKFRYI RDLYPIMFGI DV ICFLIMT FGYSAFGEGG SGNVLDDVKA SRIPVTLVVM LVGMTLAIII DRALYLRKSV VGKLIYQVLM IAFLHIWVFL VLP NMTRRS AISNHVAQAL YVIKSCYFLV SAWQIRNGYP ELCIGNLLTH SYGMTNMIAF KVFMNIPFLF ELRTAIDWTW TDTS MPLFD FFNMENFYAH IFNIKCARQF EAAYPAPRGI PKGKLVKYMM GFPIIIGVVI FIFSPLLLWS LLNQIGTISM PEKVT LRIS IEGYPPLYEM EAQGSNHDNA ELGMIKPDQL ASLNQALTDS YTTRDTNSIL RSRMSVSYLK GYTYEDILIV RFRPES EIY WPISQDSRNA MIDKLSRNTS VNFEVSLEFT RPYDPNENAA LKHSKSWLVP ISLDMTIRAK IQSALRGDPG HPILIPQ SI PAFIQVPNQG ELTLPTSIGN TIINDGNPRI NTTGMEKSDE ARAWFDSLTL NLEQGKSQNE KMWIATSEHP GDQNAKLW I KTANTTYSGR PYLQVVGFID RAFPSFLAKV FKGGVIAVYL SVILVVGRGL VRGIFTTSPS TVMFTELPNA DHLLKICLD IYLVREAKDF MLEQDLFAKL IFLFRSPATL IEWTRMSKKK QE

UniProtKB: Piezo-type mechanosensitive ion channel component 1

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 163221
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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