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

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Basic information

Entry
Database: EMDB / ID: 7128
TitleStructure of the mechanically activated ion channel Piezo1
Map dataC3 symmetry refinement mouse Piezo1 core.
Samplemouse Piezo1
  • 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
Function / homologyPiezo / Piezo non-specific cation channel, R-Ras-binding domain / Piezo domain / Piezo non-specific cation channel, R-Ras-binding domain / Piezo family / mechanosensitive ion channel activity / positive regulation of cell-cell adhesion mediated by integrin / positive regulation of integrin activation / detection of mechanical stimulus / cation channel activity ...Piezo / Piezo non-specific cation channel, R-Ras-binding domain / Piezo domain / Piezo non-specific cation channel, R-Ras-binding domain / Piezo family / mechanosensitive ion channel activity / positive regulation of cell-cell adhesion mediated by integrin / positive regulation of integrin activation / detection of mechanical stimulus / cation channel activity / cation transport / regulation of membrane potential / lamellipodium membrane / endoplasmic reticulum-Golgi intermediate compartment membrane / cellular response to mechanical stimulus / endoplasmic reticulum membrane / endoplasmic reticulum / integral component of membrane / identical protein binding / plasma membrane / Piezo-type mechanosensitive ion channel component 1
Function and homology information
SourceMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / 3.8 Å resolution
AuthorsSaotome K / Kefauver JM / Patapoutian A / Ward AB
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
Validation ReportPDB-ID: 6bpz

SummaryFull reportAbout validation report
DateDeposition: Nov 27, 2017 / Header (metadata) release: Dec 27, 2017 / Map release: Dec 27, 2017 / Last update: Jul 18, 2018

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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
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  • 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

Downloads & links

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Map

Fileemd_7128.map.gz (map file in CCP4 format, 256001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
400 pix
1.03 Å/pix.
= 412. Å
400 pix
1.03 Å/pix.
= 412. Å
400 pix
1.03 Å/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
Contour Level:0.032 (by author), 0.032 (movie #1):
Minimum - Maximum-0.07200906 - 0.13602789
Average (Standard dev.)0.000035177873 (0.0042542564)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions400400400
Origin0.0.0.
Limit399.399.399.
Spacing400400400
CellA=B=C: 412.0 Å
α=β=γ: 90.0 deg.

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
start NX/NY/NZ
NX/NY/NZ
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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Sample components

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Entire mouse Piezo1

EntireName: mouse Piezo1 / Number of components: 2

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Component #1: protein, mouse Piezo1

ProteinName: mouse Piezo1 / Recombinant expression: No
MassTheoretical: 876 kDa
SourceSpecies: Mus musculus (house mouse)
Source (engineered)Expression System: Homo sapiens (human) / Cell of expression system: HEK293F

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Component #2: protein, Piezo-type mechanosensitive ion channel component 1,Piez...

ProteinName: 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
Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 161.973531 kDa
SourceSpecies: Mus musculus (house mouse)
Source (engineered)Expression System: Homo sapiens (human)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 5 mg/ml / pH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 6 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C3 (3 fold cyclic) / Number of projections: 72627
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Refinement space: REAL
Output model

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