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- EMDB-7128: Structure of the mechanically activated ion channel Piezo1 -

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Basic information

Entry
Database: EMDB / ID: EMD-7128
TitleStructure of the mechanically activated ion channel Piezo1
Map dataC3 symmetry refinement mouse Piezo1 core.
Sample
  • Complex: mouse Piezo1
    • Protein or peptide: Piezo-type mechanosensitive ion channel component 1,Piezo-type mechanosensitive ion channel component 1,mouse Piezo1,Piezo-type mechanosensitive ion channel component 1,Piezo-type mechanosensitive ion channel component 1
Keywordsmechanosensitive ion channel / 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 / positive regulation of myotube differentiation / monoatomic cation transport / 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 / positive regulation of myotube differentiation / monoatomic cation transport / lamellipodium membrane / monoatomic cation channel activity / endoplasmic reticulum-Golgi intermediate compartment membrane / regulation of membrane potential / cellular response to mechanical stimulus / endoplasmic reticulum membrane / endoplasmic reticulum / identical protein binding / plasma membrane
Similarity search - Function
Piezo family / Piezo non-specific cation channel, R-Ras-binding domain / Piezo domain / Piezo non-specific cation channel, R-Ras-binding domain / Piezo
Similarity search - Domain/homology
Piezo-type mechanosensitive ion channel component 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsSaotome K / Kefauver JM / Patapoutian A / Ward AB
Funding support United States, 4 items
OrganizationGrant numberCountry
Ray Thomas Edwards Foundation United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS083174 United States
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)DE022358 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nature / Year: 2018
Title: Structure of the mechanically activated ion channel Piezo1.
Authors: Kei Saotome / Swetha E Murthy / Jennifer M Kefauver / Tess Whitwam / Ardem Patapoutian / Andrew B Ward /
Abstract: Piezo1 and Piezo2 are mechanically activated ion channels that mediate touch perception, proprioception and vascular development. Piezo proteins are distinct from other ion channels and their ...Piezo1 and Piezo2 are mechanically activated ion channels that mediate touch perception, proprioception and vascular development. Piezo proteins are distinct from other ion channels and their structure remains poorly defined, which impedes detailed study of their gating and ion permeation properties. Here we report a high-resolution cryo-electron microscopy structure of the mouse Piezo1 trimer. The detergent-solubilized complex adopts a three-bladed propeller shape with a curved transmembrane region containing at least 26 transmembrane helices per protomer. The flexible propeller blades can adopt distinct conformations, and consist of a series of four-transmembrane helical bundles that we term Piezo repeats. Carboxy-terminal domains line the central ion pore, and the channel is closed by constrictions in the cytosol. A kinked helical beam and anchor domain link the Piezo repeats to the pore, and are poised to control gating allosterically. The structure provides a foundation to dissect further how Piezo channels are regulated by mechanical force.
History
DepositionNov 27, 2017-
Header (metadata) releaseDec 27, 2017-
Map releaseDec 27, 2017-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.032
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.032
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6bpz
  • Surface level: 0.032
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7128.png

Downloads & links

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Map

FileDownload / File: emd_7128.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationC3 symmetry refinement mouse Piezo1 core.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 400 pix.
= 412. Å		1.03 Å/pix.
x 400 pix.
= 412. Å		1.03 Å/pix.
x 400 pix.
= 412. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.03 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.032 / Movie #1: 0.032
Minimum - Maximum-0.07200906 - 0.13602789
Average (Standard dev.)0.000035177873 (±0.0042542564)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 412.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.031.031.03
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z412.000412.000412.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0720.1360.000

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Supplemental data

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Additional map: Refinement of symmetry-expanded mouse Piezo1 blade class 1.

Fileemd_7128_additional.map
AnnotationRefinement of symmetry-expanded mouse Piezo1 blade class 1.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : mouse Piezo1

EntireName: mouse Piezo1
Components
  • Complex: mouse Piezo1
    • Protein or peptide: Piezo-type mechanosensitive ion channel component 1,Piezo-type mechanosensitive ion channel component 1,mouse Piezo1,Piezo-type mechanosensitive ion channel component 1,Piezo-type mechanosensitive ion channel component 1

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Supramolecule #1: mouse Piezo1

SupramoleculeName: mouse Piezo1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 876 KDa

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Macromolecule #1: Piezo-type mechanosensitive ion channel component 1,Piezo-type me...

MacromoleculeName: Piezo-type mechanosensitive ion channel component 1,Piezo-type mechanosensitive ion channel component 1,mouse Piezo1,Piezo-type mechanosensitive ion channel component 1,Piezo-type ...Name: Piezo-type mechanosensitive ion channel component 1,Piezo-type mechanosensitive ion channel component 1,mouse Piezo1,Piezo-type mechanosensitive ion channel component 1,Piezo-type mechanosensitive ion channel component 1
type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 161.973531 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: PNPIPNFIHC RSYLDMLKVA VFRYLFWLVL VVVFVAGATR ISIFGLGYLL ACFYLLLFGT TLLQKDTRAQ LVLWDCLILY NVTVIISKN MLSLLSCVFV EQMQSNFCWV IQLFSLVCTV KGYYDPKEMM TRDRDCLLPV EEAGIIWDSI CFFFLLLQRR I FLSHYFLH ...String:
PNPIPNFIHC RSYLDMLKVA VFRYLFWLVL VVVFVAGATR ISIFGLGYLL ACFYLLLFGT TLLQKDTRAQ LVLWDCLILY NVTVIISKN MLSLLSCVFV EQMQSNFCWV IQLFSLVCTV KGYYDPKEMM TRDRDCLLPV EEAGIIWDSI CFFFLLLQRR I FLSHYFLH VSADLKATAL QASRGFALYN AANLKSINFH RQIEEKSLAQ LKRQMKRIRA KQEKYRQSQA SRGQLQSKDP QD PSQEPGP DSPGGSSPPR RQWWRPWLDH ATVIHSGDYF LFESDSEEEE EALPEDPRPA AQSAFQMAYQ AWVTNAQTVL RQR RERARQ ERAEQLASGG DLNPDVEPVD VPEDEMAGRS HMMQRVLSTM QFLWVLGQAT VDGLTRWLRA FTKHHRTMSD VLCA ERYLL TQELLRVGEV RRGVLDQLYV GEDEATLSGP VETRDGPSTA SSGLGAEEPL SSMTDD(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)P ELEEAERFEA QQGRTLRLLR AGYQCVAAHS ELLCYFIII LNHMVTASAA SLVLPVLVFL WAMLTIPRPS KRFWMTAIVF TEVMVVTKYL FQFGFFPWNS YVVLRRYENK PYFPPRILGL EKTDSYIKY DLVQLMALFF HRSQLLCYGL WDHEEDRYPK DHCRSSVKDR EAKEEPEAKL ESQSETGTGH PKEPVLAGTP R DHIQGKGS IRSKDVIQDP PEDLKPRHTR HISIRFRRRK ETPGPKGTAV METEHEEGEG KETTERKRPR HTQEKSKFRE RM KAAGRRL QSFCVSLAQS FYQPLQRFFH DILHTKYRAA TDVYALMFLA DIVDIIIIIF GFWAFGKHSA ATDIASSLSD DQV PQAFLF MLLVQFGTMV IDRALYLRKT VLGKLAFQVV LVVAIHIWMF FILPAVTERM FSQNAVAQLW YFVKCIYFAL SAYQ IRCGY PTRILGNFLT KKYNHLNLFL FQGFRLVPFL VELRAVMDWV WTDTTLSLSN WMCVEDIYAN IFIIKCSRET EKKYP QPKG QKKKKIVKYG MGGLIILFLI AIIWFPLLFM SLIRSVVGVV NQPIDVTVTL KLGGYEPLFT MSAQQPSIVP FTPQAY EEL SQQFDPYPLA MQFISQYSPE DIVTAQIEGS SGALWRISPP SRAQMKQELY NGTADITLRF TWNFQRDLAK GGTVEYT NE KHTLELAPNS TARRQLAQLL EGRPDQSVVI PHLFPKYIRA PNGPEANPVK QLQPDEEEDY LGVRIQLRRE QVGTGASG E QAGTKASDFL EWWVIELQDC KADCNLLPMV IFSDKVSPPS LGFLAGYGIV GLYVSIVLVV GKFVRGFFSE ISHSIMFEE LPCVDRILKL CQDIFLVRET RELELEEELY AKLIFLYRSP ETMIKWTRER EKKLGAPLEV LFQ

UniProtKB: Piezo-type mechanosensitive ion channel component 1, 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

Concentration5 mg/mL
BufferpH: 8
GridModel: Quantifoil, UltrAuFoil / Material: GOLD / Mesh: 200 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 7 sec.
VitrificationCryogen name: ETHANE
Detailsmouse Piezo1 was purified in glyco-diosgenin.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 72627
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 2.0)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 2.0)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-6bpz:
Structure of the mechanically activated ion channel Piezo1

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