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- EMDB-6865: Structure of the mechanosensitive Piezo1 channel -

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Basic information

Entry
Database: EMDB / ID: EMD-6865
TitleStructure of the mechanosensitive Piezo1 channel
Map data
Sample
  • Complex: Cryo-EM map of the mechanosensitive Piezo1 channel
    • Protein or peptide: Piezo-type mechanosensitive ion channel component 1
Function / homology
Function and homology information


mechanosensitive monoatomic cation channel activity / positive regulation of cell-cell adhesion mediated by integrin / detection of mechanical stimulus / mechanosensitive monoatomic ion channel activity / positive regulation of integrin activation / positive regulation of myotube differentiation / lamellipodium membrane / monoatomic cation transport / monoatomic cation channel activity / regulation of membrane potential ...mechanosensitive monoatomic cation channel activity / positive regulation of cell-cell adhesion mediated by integrin / detection of mechanical stimulus / mechanosensitive monoatomic ion channel activity / positive regulation of integrin activation / positive regulation of myotube differentiation / lamellipodium membrane / monoatomic cation transport / monoatomic cation channel activity / regulation of membrane potential / endoplasmic reticulum-Golgi intermediate compartment membrane / 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: 3.97 Å
AuthorsZhao Q / Zhou H / Chi S / Wang Y / Wang J / Geng J / Wu K / Liu W / Zhang T / Dong M-Q ...Zhao Q / Zhou H / Chi S / Wang Y / Wang J / Geng J / Wu K / Liu W / Zhang T / Dong M-Q / Li X / Xiao B
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31630090 China
CitationJournal: Nature / Year: 2018
Title: Structure and mechanogating mechanism of the Piezo1 channel.
Authors: Qiancheng Zhao / Heng Zhou / Shaopeng Chi / Yanfeng Wang / Jianhua Wang / Jie Geng / Kun Wu / Wenhao Liu / Tingxin Zhang / Meng-Qiu Dong / Jiawei Wang / Xueming Li / Bailong Xiao /
Abstract: The mechanosensitive Piezo channels function as key eukaryotic mechanotransducers. However, their structures and mechanogating mechanisms remain unknown. Here we determine the three-bladed, propeller- ...The mechanosensitive Piezo channels function as key eukaryotic mechanotransducers. However, their structures and mechanogating mechanisms remain unknown. Here we determine the three-bladed, propeller-like electron cryo-microscopy structure of mouse Piezo1 and functionally reveal its mechanotransduction components. Despite the lack of sequence repetition, we identify nine repetitive units consisting of four transmembrane helices each-which we term transmembrane helical units (THUs)-which assemble into a highly curved blade-like structure. The last transmembrane helix encloses a hydrophobic pore, followed by three intracellular fenestration sites and side portals that contain pore-property-determining residues. The central region forms a 90 Å-long intracellular beam-like structure, which undergoes a lever-like motion to connect THUs to the pore via the interfaces of the C-terminal domain, the anchor-resembling domain and the outer helix. Deleting extracellular loops in the distal THUs or mutating single residues in the beam impairs the mechanical activation of Piezo1. Overall, Piezo1 possesses a unique 38-transmembrane-helix topology and designated mechanotransduction components, which enable a lever-like mechanogating mechanism.
History
DepositionDec 22, 2017-
Header (metadata) releaseJan 31, 2018-
Map releaseJan 31, 2018-
UpdateJan 29, 2020-
Current statusJan 29, 2020Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5z10
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6865.png

Downloads & links

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Map

FileDownload / File: emd_6865.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.32 Å
Density
Contour LevelBy AUTHOR: 0.027 / Movie #1: 0.04
Minimum - Maximum-0.19287774 - 0.30006224
Average (Standard dev.)0.0008083889 (±0.006078111)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 369.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.321.321.32
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z369.600369.600369.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-128-128-128
NX/NY/NZ256256256
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-0.1930.3000.001

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Supplemental data

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Sample components

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Entire : Cryo-EM map of the mechanosensitive Piezo1 channel

EntireName: Cryo-EM map of the mechanosensitive Piezo1 channel
Components
  • Complex: Cryo-EM map of the mechanosensitive Piezo1 channel
    • Protein or peptide: Piezo-type mechanosensitive ion channel component 1

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Supramolecule #1: Cryo-EM map of the mechanosensitive Piezo1 channel

SupramoleculeName: Cryo-EM map of the mechanosensitive Piezo1 channel / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293T

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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: Mus musculus (house mouse)
Molecular weightTheoretical: 292.320656 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEPHVLGAGL YWLLLPCTLL AASLLRFNAL SLVYLLFLLL LPWLPGPSRH SIPGHTGRLL RALLCLSLLF LVAHLAFQIC LHTVPHLDQ FLGQNGSLWV KVSQHIGVTR LDLKDIFNTT RLVAPDLGVL LASSLCLGLC GRLTRKAGQS RRTQELQDDD D DDDDDDED ...String:
MEPHVLGAGL YWLLLPCTLL AASLLRFNAL SLVYLLFLLL LPWLPGPSRH SIPGHTGRLL RALLCLSLLF LVAHLAFQIC LHTVPHLDQ FLGQNGSLWV KVSQHIGVTR LDLKDIFNTT RLVAPDLGVL LASSLCLGLC GRLTRKAGQS RRTQELQDDD D DDDDDDED IDAAPAVGLK GAPALATKRR LWLASRFRVT AHWLLMTSGR TLVIVLLALA GIAHPSAFSS IYLVVFLAIC TW WSCHFPL SPLGFNTLCV MVSCFGAGHL ICLYCYQTPF IQDMLPPGNI WARLFGLKNF VDLPNYSSPN ALVLNTKHAW PIY VSPGIL LLLYYTATSL LKLHKSCPSE LRKETPREDE EHELELDHLE PEPQARDATQ GEMPMTTEPD LDNCTVHVLT SQSP VRQRP VRPRLAELKE MSPLHGLGHL IMDQSYVCAL IAMMVWSIMY HSWLTFVLLL WACLIWTVRS RHQLAMLCSP CILLY GLTL CCLRYVWAME LPELPTTLGP VSLHQLGLEH TRYPCLDLGA MLLYLLTFWL LLRQFVKEKL LKKQKVPAAL LEVTVA DTE PTQTQTLLRS LGELVTGIYV KYWIYVCAGM FIVVSFAGRL VVYKIVYMFL FLLCLTLFQV YYTLWRKLLR VFWWLVV AY TMLVLIAVYT FQFQDFPTYW RNLTGFTDEQ LGDLGLEQFS VSELFSSILI PGFFLLACIL QLHYFHRPFM QLTDLEHV P PPGTRHPRWA HRQDAVSEAP LLEHQEEEEV FREDGQSMDG PHQATQVPEG TASKWGLVAD RLLDLAASFS AVLTRIQVF VRRLLELHVF KLVALYTVWV ALKEVSVMNL LLVVLWAFAL PYPRFRPMAS CLSTVWTCII IVCKMLYQLK IVNPHEYSSN CTEPFPNNT NLQPLEINQS LLYRGPVDPA NWFGVRKGYP NLGYIQNHLQ ILLLLVFEAV VYRRQEHYRR QHQQAPLPAQ A VCADGTRQ RLDQDLLSCL KYFINFFFYK FGLEICFLMA VNVIGQRMNF MVILHGCWLV AILTRRRREA IARLWPNYCL FL TLFLLYQ YLLCLGMPPA LCIDYPWRWS KAIPMNSALI KWLYLPDFFR APNSTNLISD FLLLLCASQQ WQVFSAERTE EWQ RMAGIN TDHLEPLRGE PNPIPNFIHC RSYLDMLKVA VFRYLFWLVL VVVFVAGATR ISIFGLGYLL ACFYLLLFGT TLLQ KDTRA QLVLWDCLIL YNVTVIISKN MLSLLSCVFV EQMQSNFCWV IQLFSLVCTV KGYYDPKEMM TRDRDCLLPV EEAGI IWDS ICFFFLLLQR RIFLSHYFLH VSADLKATAL QASRGFALYN AANLKSINFH RQIEEKSLAQ LKRQMKRIRA KQEKYR QSQ ASRGQLQSKD PQDPSQEPGP DSPGGSSPPR RQWWRPWLDH ATVIHSGDYF LFESDSEEEE EALPEDPRPA AQSAFQM AY QAWVTNAQTV LRQRRERARQ ERAEQLASGG DLNPDVEPVD VPEDEMAGRS HMMQRVLSTM QFLWVLGQAT VDGLTRWL R AFTKHHRTMS DVLCAERYLL TQELLRVGEV RRGVLDQLYV GEDEATLSGP VETRDGPSTA SSGLGAEEPL SSMTDDTSS PLSTGYNTRS GSEEIVTDAG DLQAGTSLHG SQELLANART RMRTASELLL DRRLHIPELE EAERFEAQQG RTLRLLRAGY QCVAAHSEL LCYFIIILNH MVTASAASLV LPVLVFLWAM LTIPRPSKRF WMTAIVFTEV MVVTKYLFQF GFFPWNSYVV L RRYENKPY FPPRILGLEK TDSYIKYDLV QLMALFFHRS QLLCYGLWDH EEDRYPKDHC RSSVKDREAK EEPEAKLESQ SE TGTGHPK EPVLAGTPRD HIQGKGSIRS KDVIQDPPED LKPRHTRHIS IRFRRRKETP GPKGTAVMET EHEEGEGKET TER KRPRHT QEKSKFRERM KAAGRRLQSF CVSLAQSFYQ PLQRFFHDIL HTKYRAATDV YALMFLADIV DIIIIIFGFW AFGK HSAAT DIASSLSDDQ VPQAFLFMLL VQFGTMVIDR ALYLRKTVLG KLAFQVVLVV AIHIWMFFIL PAVTERMFSQ NAVAQ LWYF VKCIYFALSA YQIRCGYPTR ILGNFLTKKY NHLNLFLFQG FRLVPFLVEL RAVMDWVWTD TTLSLSNWMC VEDIYA NIF IIKCSRETEK KYPQPKGQKK KKIVKYGMGG LIILFLIAII WFPLLFMSLI RSVVGVVNQP IDVTVTLKLG GYEPLFT MS AQQPSIVPFT PQAYEELSQQ FDPYPLAMQF ISQYSPEDIV TAQIEGSSGA LWRISPPSRA QMKQELYNGT ADITLRFT W NFQRDLAKGG TVEYTNEKHT LELAPNSTAR RQLAQLLEGR PDQSVVIPHL FPKYIRAPNG PEANPVKQLQ PDEEEDYLG VRIQLRREQV GTGASGEQAG TKASDFLEWW VIELQDCKAD CNLLPMVIFS DKVSPPSLGF LAGYGIVGLY VSIVLVVGKF VRGFFSEIS HSIMFEELPC VDRILKLCQD IFLVRETREL ELEEELYAKL IFLYRSPETM IKWTRERE

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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

Concentration0.18 mg/mL
BufferpH: 7.2
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV
Details: After a 15 sec waiting time, the grids were blotted for 3.5 sec and plunged into liquid ethane.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus min: 3.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus min: 1.5 µm / Nominal magnification: 22500
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-32 / Average exposure time: 8.0 sec. / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: RELION (ver. 1.4)
Startup modelType of model: OTHER / Details: cylinder
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: RELION (ver. 1.4)
Final 3D classificationSoftware - Name: RELION (ver. 1.4)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 1.4)
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.97 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 238529
FSC plot (resolution estimation)

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