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- EMDB-64384: Structure of C. elegans piezo channel isoform k -

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Basic information

Entry
Database: EMDB / ID: EMD-64384
TitleStructure of C. elegans piezo channel isoform k
Map data
Sample
  • Complex: C. elegans Piezo channel isoform k
    • Protein or peptide: Isoform k of 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: 3.8 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_64384.png

Downloads & links

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Map

FileDownload / File: emd_64384.map.gz / Format: CCP4 / Size: 536.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.97 Å/pix.
x 520 pix.
= 504.4 Å		0.97 Å/pix.
x 520 pix.
= 504.4 Å		0.97 Å/pix.
x 520 pix.
= 504.4 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.97 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.36044368 - 1.1825664
Average (Standard dev.)-0.0019656979 (±0.038053907)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions520520520
Spacing520520520
CellA=B=C: 504.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: sharpened

Fileemd_64384_additional_1.map
Annotationsharpened
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

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Half map: #1

Fileemd_64384_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_64384_half_map_2.map
Projections & Slices
AxesZYX

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Sample components

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Entire : C. elegans Piezo channel isoform k

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

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Supramolecule #1: C. elegans Piezo channel isoform k

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

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Macromolecule #1: Isoform k of Piezo-type mechanosensitive ion channel component 1

MacromoleculeName: Isoform k of 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: 191.812578 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MLQLKFFHGP WSRATSPRRA ENDPPTSTTE AAAVASTSGT QGRAHAAGDT LVKKLHKLAN QTIELLWRFF EVHISKIVFV IIAIFIANN INALYIPLVI LLSLAICLPS AADGIFSLFM CAYLFLVALS KMIYQLDIVP ELSQIDRGVG ADNCSHGNIS M PEWFGLKK ...String:
MLQLKFFHGP WSRATSPRRA ENDPPTSTTE AAAVASTSGT QGRAHAAGDT LVKKLHKLAN QTIELLWRFF EVHISKIVFV IIAIFIANN INALYIPLVI LLSLAICLPS AADGIFSLFM CAYLFLVALS KMIYQLDIVP ELSQIDRGVG ADNCSHGNIS M PEWFGLKK EVEGTEPIYM LFGVIVSIIA LAFQSIVIYR QRHYRASLGL PESMRAKVFP DFHHSHFDRS LKNAIQFLID YG FYKFGLE ITMIAIGIDI FNRMDALAAI QCFWLVLFAL NKRVFVRRIW VFYVIYMAIL YPLQFFSYVG LPPDSCIEYP WSY WIPSYS DDARFNLSYL LNLSIYGVNW PSAYLIGDFF VLLLASCQLA VFRREGEDND SIYNDGNFVI KPENPQYDFI DTKK SYVDY FKSFVFHYGH WITLMSTLAA GIAGTSLFAL GYIIFTLTML WSGNNLYVMN STLRSFEHTL KRWNALLGYT LFTIT MKVC LQIFGCVFLS WFDQSGGWGK TLCIVRQLFS ITCVNNECHV LKELEDFSKA CAVETKEGNI GFDVIALSFL VFQIRI FHS WYFQHCMVEY RSEVILANRG AVLKNQLIEK EMKEQNEQQK AKFNDIRRRT EAIRERYQKQ IERGAAERDF EPVTYGH AK RAGDYYMFKY DPENDDLVEP VDSFVPEVDP KATAYDRLDP GQIMYAATAH DLDLAKTVQQ VKKGDTIKDP DSRALIAV S EPEARKPGGT EETDGDEDED NKDSKVESTA KFIQKMIASA LDLCSVTLNK LCREHRYVGF VLSKEKQKLK SGHSESLSN TSRKLTDIRS AVDLPSLQLV QSANDVEKME TAVSVDWQQK SSATRLLNAV VNCIGAHTDI LCYFFAIMTQ VMTGGLITLP LPLMSLFWG NLSNPRPSKF FWVTMITYTE CVIVIKFVCQ FAFMPYNSIT WRTEHQMDPM SLDKLFGVSQ RDSFALWDIV L LFSLFFHR YMLRKLGLWK DANLTDTFTL KEEPRSASGS DTGSPKKIAQ EPKVVVTQSD TLEGTSGGEI VIPSDPNAVS NM EELDCEP PIPEKQSGPI GRFIHQLFHP KFRYIRDLYP IMFGIDVICF LIMTFGYSAF GEGGSGNVLD DVKASRIPVT LVV MLVGMT LAIIIDRALY LRKSVVGKLI YQVLMIAFLH IWVFLVLPNM TRRSAISNHV AQALYVIKSC YFLVSAWQIR NGYP ELCIG NLLTHSYGMT NMIAFKVFMN IPFLFELRTA IDWTWTDTSM PLFDFFNMEN FYAHIFNIKC ARQFEAAYPA PRGIP KGKL VKYMMGFPII IGVVIFIFSP LLLWSLLNQI GTISMPEKVT LRISIEGYPP LYEMEAQGSN HDNAELGMIK PDQLAS LNQ ALTDSYTTRD TNSILRSRMS VSYLKGYTYE DILIVRFRPE SEIYWPISQD SRNAMIDKLS RNTSVNFEVS LEFTRPY DP NENAALKHSK SWLVPISLDM TIRAKIQSAL RGDPGHPILI PQSIPAFIQV PNQGELTLPT SIGNTIINDG NPRINTTG M EKSDEARAWF DSLTLNLEQG KSQNEKMWIA TSEHPGDQNA KLWIKTANTT YSGRPYLQVV GFIDRAFPSF LAKVFKGGV IAVYLSVILV VGRGLVRGIF TTSPSTVMFT ELPNADHLLK ICLDIYLVRE AKDFMLEQDL FAKLIFLFRS PATLIEWTRM SKKKQE

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

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.9 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: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 93555
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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