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- EMDB-60481: Human PIEZO1-A1988V -

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Basic information

Entry
Database: EMDB / ID: EMD-60481
TitleHuman PIEZO1-A1988V
Map data
Sample
  • Complex: human PIEZO1-A1988V
    • Protein or peptide: Piezo-type mechanosensitive ion channel component 1
  • Ligand: (1S)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(octadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate
KeywordsHuman PIEZO1 / MEMBRANE PROTEIN
Function / homology
Function and homology information


mechanosensitive monoatomic cation channel activity / cuticular plate / positive regulation of cell-cell adhesion mediated by integrin / detection of mechanical stimulus / positive regulation of integrin activation / mechanosensitive monoatomic ion channel activity / stereocilium / Mechanical load activates signaling by PIEZO1 and integrins in osteocytes / positive regulation of myotube differentiation / lamellipodium membrane ...mechanosensitive monoatomic cation channel activity / cuticular plate / positive regulation of cell-cell adhesion mediated by integrin / detection of mechanical stimulus / positive regulation of integrin activation / mechanosensitive monoatomic ion channel activity / stereocilium / Mechanical load activates signaling by PIEZO1 and integrins in osteocytes / positive regulation of myotube differentiation / lamellipodium membrane / monoatomic cation transport / monoatomic cation channel activity / endoplasmic reticulum-Golgi intermediate compartment membrane / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / regulation of membrane potential / cellular response to mechanical stimulus / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / endoplasmic reticulum membrane / endoplasmic reticulum / 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
Similarity search - Domain/homology
Piezo-type mechanosensitive ion channel component 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsZhang MF
Funding support China, 1 items
OrganizationGrant numberCountry
Other government China
CitationJournal: Elife / Year: 2024
Title: Structure of human PIEZO1 and its slow inactivating channelopathy mutants.
Authors: Shan Y / Guo X / Zhang M / Chen M / Li Y / Zhang MF / Pei D
History
DepositionJun 8, 2024-
Header (metadata) releaseJan 29, 2025-
Map releaseJan 29, 2025-
UpdateJan 29, 2025-
Current statusJan 29, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_60481.png

Downloads & links

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Map

FileDownload / File: emd_60481.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 512 pix.
= 434.688 Å		0.85 Å/pix.
x 512 pix.
= 434.688 Å		0.85 Å/pix.
x 512 pix.
= 434.688 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.849 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.2863488 - 0.5251627
Average (Standard dev.)-0.0005501656 (±0.013332605)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 434.688 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_60481_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_60481_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 : human PIEZO1-A1988V

EntireName: human PIEZO1-A1988V
Components
  • Complex: human PIEZO1-A1988V
    • Protein or peptide: Piezo-type mechanosensitive ion channel component 1
  • Ligand: (1S)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(octadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate

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Supramolecule #1: human PIEZO1-A1988V

SupramoleculeName: human PIEZO1-A1988V / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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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: Homo sapiens (human)
Molecular weightTheoretical: 223.939828 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ELVKGVYAKY WIYVCAGMFI VVSFAGRLVV YKIVYMFLFL LCLTLFQVYY SLWRKLLKAF WWLVVAYTML VLIAVYTFQF QDFPAYWRN LTGFTDEQLG DLGLEQFSVS ELFSSILVPG FFLLACILQL HYFHRPFMQL TDMEHVSLPG TRLPRWAHRQ D AVSGTPLL ...String:
ELVKGVYAKY WIYVCAGMFI VVSFAGRLVV YKIVYMFLFL LCLTLFQVYY SLWRKLLKAF WWLVVAYTML VLIAVYTFQF QDFPAYWRN LTGFTDEQLG DLGLEQFSVS ELFSSILVPG FFLLACILQL HYFHRPFMQL TDMEHVSLPG TRLPRWAHRQ D AVSGTPLL REEQQEHQQQ QQEEEEEEED SRDEGLGVAT PHQATQVPEG AAKWGLVAER LLELAAGFSD VLSRVQVFLR RL LELHVFK LVALYTVWVA LKEVSVMNLL LVVLWAFALP YPRFRPMASC LSTVWTCVII VCKMLYQLKV VNPQEYSSNC TEP FPNSTN LLPTEISQSL LYRGPVDPAN WFGVRKGFPN LGYIQNHLQV LLLLVFEAIV YRRQEHYRRQ HQLAPLPAQA VFAS GTRQQ LDQDLLGCLK YFINFFFYKF GLEICFLMAV NVIGQRMNFL VTLHGCWLVA ILTRRHRQAI ARLWPNYCLF LALFL LYQY LLCLGMPPAL CIDYPWRWSR AVPMNSALIK WLYLPDFFRA PNSTNLISDF LLLLCASQQW QVFSAERTEE WQRMAG VNT DRLEPLRGEP NPVPNFIHCR SYLDMLKVAV FRYLFWLVLV VVFVTGATRI SIFGLGYLLA CFYLLLFGTA LLQRDTR AR LVLWDCLILY NVTVIISKNM LSLLACVFVE QMQTGFCWVI QLFSLVCTVK GYYDPKEMMD RDQDCLLPVE EAGIIWDS V CFFFLLLQRR VFLSHYYLHV RADLQATALL ASRGFALYNA ANLKSIDFHR RIEEKSLAQL KRQMERIRAK QEKHRQGRV DRSRPQDTLG PKDPGLEPGP DSPGGSSPPR RQWWRPWLDH ATVIHSGDYF LFESDSEEEE EAVPEDPRPS AQSAFQLAYQ AWVTNAQAV LRRRQQEQEQ ARQEQAGQLP TGGGPSQEVE PAEGPEEAAA GRSHVVQRVL STAQFLWMLG QALVDELTRW L QEFTRHHG TMSDVLRAER YLLTQELLQG GEVHRGVLDQ LYTSQAEATL PGPTEAPNAP STVSSGLGAE EPLSSMTDDM GS PLSTGYH TRSGSEEAVT DPGEREAGAS LYQGLMRTAS ELLLDRRLRI PELEEAELFA EGQGRALRLL RAVYQCVAAH SEL LCYFII ILNHMVTASA GSLVLPVLVF LWAMLSIPRP SKRFWMTAIV FTEIAVVVKY LFQFGFFPWN SHVVLRRYEN KPYF PPRIL GLEKTDGYIK YDLVQLMALF FHRSQLLCYG LWDHEEDSPS KEHDKSGEEE QGAEEGPGVP AATTEDHIQV EARVG PTDG TPEPQVELRP RDTRRISLRF RRRKKEGPAR KGAAAIEAED REEEEGEEEK EAPTGREKRP SRSGGRVRAA GRRLQG FCL SLAQGTYRPL RRFFHDILHT KYRAATDVYA LMFLADVVDF IIIIFGFWAF GKHSAVTDIT SSLSDDQVPE AFLVMLL IQ FSTMVVDRAL YLRKTVLGKL AFQVALVLAI HLWMFFILPA VTERMFNQNV VAQLWYFVKC IYFALSAYQI RCGYPTRI L GNFLTKKYNH LNLFLFQGFR LVPFLVELRA VMDWVWTDTT LSLSSWMCVE DIYANIFIIK CSRETEKKYP QPKGQKKKK IVKYGMGGLI ILFLIAIIWF PLLFMSLVRS VVGVVNQPID VTVTLKLGGY EPLFTMSAQQ PSIIPFTAQA YEELSRQFDP QPLAMQFIS QYSPEDIVTA QIEGSSGALW RISPPSRAQM KRELYNGTAD ITLRFTWNFQ RDLAKGGTVE YANEKHMLAL A PNSTARRQ LASLLEGTSD QSVVIPNLFP KYIRAPNGPE ANPVKQLQPN EEADYLGVRI QLRREQGAGA TGFLEWWVIE LQ ECRTDCN LLPMVIFSDK VSPPSLGFLA GYGIMGLYVS IVLVIGKFVR GFFSEISHSI MFEELPCVDR ILKLCQDIFL VRE TRELEL EEELYAKLIF LYRSPETMIK WTREKE

UniProtKB: Piezo-type mechanosensitive ion channel component 1

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Macromolecule #2: (1S)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(octadeca...

MacromoleculeName: (1S)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(octadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate
type: ligand / ID: 2 / Number of copies: 3 / Formula: L9Q
Molecular weightTheoretical: 746.05 Da
Chemical component information

ChemComp-L9Q:
(1S)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(octadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI 10
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 32000
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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