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- EMDB-64386: Focus-refined map of C. elegans piezo channel -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-64386
TitleFocus-refined map of C. elegans piezo channel
Map data
Sample
  • Complex: C. elegans Piezo channel
    • Protein or peptide: Piezo-type mechanosensitive ion channel
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: 3.62 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) releaseMar 4, 2026-
Map releaseMar 4, 2026-
UpdateMar 4, 2026-
Current statusMar 4, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64386.png

Downloads & links

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Map

FileDownload / File: emd_64386.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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.21815388 - 0.4887566
Average (Standard dev.)-0.00011612625 (±0.010767459)
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_64386_additional_1.map
Annotationsharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_64386_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_64386_half_map_2.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 : C. elegans Piezo channel

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

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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

MacromoleculeName: Piezo-type mechanosensitive ion channel / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
SequenceString: MTVPPLLKSC VVKLLLPAAL LAAAIIRPSF LSIGYVLLAL VSAVLPPIRK SLALPKLVGT FVIITFLFCL AVALGVGSYQ ISEQVVHKND RTYICNRSDT TLFRSIGLVR FHPTGTFEST RAFLPEIIAT SAALLTIIIV MFLSHRDEQL DVVGDVVTVR SESGREQRRQ ...String:
MTVPPLLKSC VVKLLLPAAL LAAAIIRPSF LSIGYVLLAL VSAVLPPIRK SLALPKLVGT FVIITFLFCL AVALGVGSYQ ISEQVVHKND RTYICNRSDT TLFRSIGLVR FHPTGTFEST RAFLPEIIAT SAALLTIIIV MFLSHRDEQL DVVGDVVTVR SESGREQRRQ RKLAAIMWSA IGNSLRRLTN FVLFLFTAYV GIVKPSLSNS IYFLAFLFIS TWWSTYTPLR HGVYNQIKKF LIFYSALHFL VLYTYQIPIV HHSWLPTGSF LPRLFGLTVL MDSSCPEWWK FPFVAPDFND DDLIMKWPLY ANPIVVLVFF YLTVAQYKFT RNGSREYIDD NEYGSSVHEE RFVSAGTVET NVDDVGQLIS ISESTASAPS GRGRGNTLLL SNASSSANDD EQGRARSRSP LRNGEEQGSI PLRKVTSQVV DRNKLSNIFN TTAPGDKESA ASKGMIAVMT FVIFHSYSIA LTAMMTWALL YHSIFGLILL ILTCILWIFR DTRKSSFAMA PIILMYIEFL LILQYFLSMD IHAEIGDPAW MNFVGIEWTT LPVHAVIILC VQTLLTLPVF LLLRLARREK FYESLSDYER QRRINSYGTF GASKTGAGGV AVAKFQDPKS RKFAAFVEYL SNKVSVYFIF VVSVVLLVVS TCFAPNFYNI LFFALWALNL IYLKFSFRLY RGLAYAFWLT LTFYTSIVII ALYIYQFPGV SQWIIRNTSL SQEWLNAIGL VDFRAIGESG ALFLQLLAPI ALFVVTMLQL KFFHGPWSRA TSPRRAENDP PTSTTEAAAV ASTSGTQGRA HAAGDTLVKK LHKLANQTIE LLWRFFEVHI SKIVFVIIAI FIANNINALY IPLVILLSLA ICLPSAADGI FSLFMCAYLF LVALSKMIYQ LDIVPELSQI DRGVGADNCS HGNISMPEWF GLKKEVEGTE PIYMLFGVIV SIIALAFQSI VIYRQRHYRA SLGLPESMRA KVFPDFHHSH FDRSLKNAIQ FLIDYGFYKF GLEITMIAIG IDIFNRMDAL AAIQCFWLVL FALNKRVFVR RIWVFYVIYM AILYPLQFFS YVGLPPDSCI EYPWSYWIPS YSDDARFNLS YLLNLSIYGV NWPSAYLIGD FFVLLLASCQ LAVFRREGED NDSIYNDGNF VIKPENPQYD FIDTKKSYVD YFKSFVFHYG HWITLMSTLA AGIAGTSLFA LGYIIFTLTM LWSGNNLYVM NSTLRSFEHT LKRWNALLGY TLFTITMKVC LQIFGCVFLS WFDQSGGWGK TLCIVRQLFS ITCVNNECHV LKELEDFSKA CAVETKEGNI GFDVIALSFL VFQIRIFHSW YFQHCMVEYR SEVILANRGA VLKNQLIEKE MKEQNEQQKA KFNDIRRRTE AIRERYQKQI ERGAAERDFE PVTYGHAKRA GDYYMFKYDP ENDDLVEPVD SFVPEVDPKA TAYDRLDPGQ IMYAATAHDL DLAKTVQQVK KGDTIKDPDS RALIAVSEPE ARKPGGTEET DGDEDEDNKD SKVESTAKFI QKMIASALDL CSVTLNKLCR EHRYVGFVLS KEKQKLKSGH SESLSNTSRK LTDIRSAVDL PSLQLVQSAN DVEKMETAVS VDWQQKSSAT RLLNAVVNCI GAHTDILCYF FAIMTQVMTG GLITLPLPLM SLFWGNLSNP RPSKFFWVTM ITYTECVIVI KFVCQFAFMP YNSITWRTEH QMDPMSLDKL FGVSQRDSFA LWDIVLLFSL FFHRYMLRKL GLWKDANLTD TFTLKEEPRS ASGSDTGSPK KIAQEPKVVV TQSDTLEGTS GGEIVIPSDP NAVSNMEELD CEPPIPEKQS GPIGRFIHQL FHPKFRYIRD LYPIMFGIDV ICFLIMTFGY SAFGEGGSGN VLDDVKASRI PVTLVVMLVG MTLAIIIDRA LYLRKSVVGK LIYQVLMIAF LHIWVFLVLP NMTRRSAISN HVAQALYVIK SCYFLVSAWQ IRNGYPELCI GNLLTHSYGM TNMIAFKVFM NIPFLFELRT AIDWTWTDTS MPLFDFFNME NFYAHIFNIK CARQFEAAYP APRGIPKGKL VKYMMGFPII IGVVIFIFSP LLLWSLLNQI GTISMPEKVT LRISIEGYPP LYEMEAQGSN HDNAELGMIK PDQLASLNQA LTDSYTTRDT NSILRSRMSV SYLKGYTYED ILIVRFRPES EIYWPISQDS RNAMIDKLSR NTSVNFEVSL EFTRPYDPNE NAALKHSKSW LVPISLDMTI RAKIQSALRG DPGHPILIPQ SIPAFIQVPN QGELTLPTSI GNTIINDGNP RINTTGMEKS DEARAWFDSL TLNLEQGKSQ NEKMWIATSE HPGDQNAKLW IKTANTTYSG RPYLQVVGFI DRAFPSFLAK VFKGGVIAVY LSVILVVGRG LVRGIFTTSP STVMFTELPN ADHLLKICLD 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: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.62 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 151385
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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