[English] 日本語
Yorodumi
- EMDB-60481: Human PIEZO1-A1988V -

+
Open data


ID or keywords:

Loading...

-
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 / Piezo TM1-24 / Piezo, THU9 and anchor domain
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
Citation
Journal: Elife / Year: 2025
Title: Structure of human PIEZO1 and its slow-inactivating channelopathy mutants.
Authors: Yuanyue Shan / Xinyi Guo / Mengmeng Zhang / Meiyu Chen / Ying Li / Mingfeng Zhang / Duanqing Pei /
Abstract: PIEZO channels transmit mechanical force signals to cells, allowing them to make critical decisions during development and in pathophysiological conditions. Their fast/slow inactivation modes have ...PIEZO channels transmit mechanical force signals to cells, allowing them to make critical decisions during development and in pathophysiological conditions. Their fast/slow inactivation modes have been implicated in mechanopathologies but remain poorly understood. Here, we report several near-atomic resolution cryo-EM structures of fast-inactivating wild-type human PIEZO1 (hPIEZO1) and its slow-inactivating channelopathy mutants with or without its auxiliary subunit MDFIC. Our results suggest that hPIEZO1 has a more flattened and extended architecture than curved mouse PIEZO1 (mPIEZO1). The multi-lipidated MDFIC subunits insert laterally into the hPIEZO1 pore module like mPIEZO1, resulting in a more curved and extended state. Interestingly, the high-resolution structures suggest that the pore lipids, which directly seal the central hydrophobic pore, may be involved in the rapid inactivation of hPIEZO1. While the severe hereditary erythrocytosis mutant R2456H significantly slows down the inactivation of hPIEZO1, the hPIEZO1-R2456H-MDFIC complex shows a more curved and contracted structure with an inner helix twist due to the broken link between the pore lipid and R2456H. These results suggest that the pore lipids may be involved in the mechanopathological rapid inactivation mechanism of PIEZO channels.
#1: Journal: 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-
UpdateAug 27, 2025-
Current statusAug 27, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Downloads & links

-
Map

FileDownload / File: emd_60481.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.849 Å
Density
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 °

-
Supplemental data

-
Sample components

-
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

-
Supramolecule #1: human PIEZO1-A1988V

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

-
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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
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

+
Image processing

CTF correctionType: PHASE FLIPPING ONLY
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more