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- EMDB-74281: C. elegans PEZO-1 Isoform G -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-74281
TitleC. elegans PEZO-1 Isoform G
Map data
Sample
  • Complex: C. elegans PEZO-1 Isoform G
    • Protein or peptide: Piezo-type mechanosensitive ion channel component 1
KeywordsPEZO-1 / Piezo / MEMBRANE PROTEIN / mechanosensation
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: 3.5 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_74281.png

Downloads & links

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Map

FileDownload / File: emd_74281.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: 0.0561
Minimum - Maximum-0.37105864 - 0.54477394
Average (Standard dev.)-0.000055105924 (±0.008631997)
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_74281_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_74281_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 G

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

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

SupramoleculeName: C. elegans PEZO-1 Isoform G / 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

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 / Cs: 2.7 mm / 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: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 77342
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: AlphaFold / Chain - Initial model type: in silico model / Details: Used for refinement into the map
Output model

PDB-9zis:
C. elegans PEZO-1 Isoform G

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