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- EMDB-74283: C. elegans PEZO-1 Isoform K -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-74283
TitleC. elegans PEZO-1 Isoform K
Map data
Sample
  • Complex: C. elegans PEZO-1 Isoform K
    • Protein or peptide: Piezo-type mechanosensitive ion channel component 1
KeywordsPEZO-1 / Piezo channels / MEMBRANE PROTEIN / mechanosensitive ion channels / C. elegans / isoforms
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: 3.1 Å
AuthorsBell B / Baker ML / Vasquez V
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM153208 United States
CitationJournal: To Be Published
Title: Structures of invertebrate PEZO-1 isoforms with a compact architecture and a dispensable pore-distal N-terminal blade
Authors: Bell B / Jaramillo-Granada AM / Orlin DJ / Weng W-H / Wen H / Sotomayor M / Chesler AT / Baker ML / Cordero-Morales JF / Vasquez V
History
DepositionDec 4, 2025-
Header (metadata) releaseDec 24, 2025-
Map releaseDec 24, 2025-
UpdateDec 24, 2025-
Current statusDec 24, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_74283.png

Downloads & links

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Map

FileDownload / File: emd_74283.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 448 pix.
= 483.84 Å		1.08 Å/pix.
x 448 pix.
= 483.84 Å		1.08 Å/pix.
x 448 pix.
= 483.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0689
Minimum - Maximum-0.39261514 - 0.6475552
Average (Standard dev.)-0.00022829643 (±0.009589476)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 483.84003 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_74283_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_74283_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 PEZO-1 Isoform K

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

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Supramolecule #1: C. elegans PEZO-1 Isoform K

SupramoleculeName: C. elegans PEZO-1 Isoform K / 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: 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 KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / 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: 2.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 158413
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: other / Details: PEZO-1 Isoform G model
Output model

PDB-9zit:
C. elegans PEZO-1 Isoform K

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