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- PDB-3jac: Cryo-EM study of a channel -

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Basic information

Entry
Database: PDB / ID: 3jac
TitleCryo-EM study of a channel
ComponentsPiezo-type mechanosensitive ion channel component 1
KeywordsMETAL TRANSPORT / Cryo-EM / single particle
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 / lamellipodium membrane / monoatomic cation transport ...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 / lamellipodium membrane / monoatomic cation transport / monoatomic cation channel activity / endoplasmic reticulum-Golgi intermediate compartment membrane / regulation of membrane potential / 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, 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 speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / negative staining / cryo EM / Resolution: 4.8 Å
AuthorsGe, J. / Li, W. / Zhao, Q. / Li, N. / Xiao, B. / Gao, N. / Yang, M.
CitationJournal: Nature / Year: 2015
Title: Architecture of the mammalian mechanosensitive Piezo1 channel.
Authors: Jingpeng Ge / Wanqiu Li / Qiancheng Zhao / Ningning Li / Maofei Chen / Peng Zhi / Ruochong Li / Ning Gao / Bailong Xiao / Maojun Yang /
Abstract: Piezo proteins are evolutionarily conserved and functionally diverse mechanosensitive cation channels. However, the overall structural architecture and gating mechanisms of Piezo channels have ...Piezo proteins are evolutionarily conserved and functionally diverse mechanosensitive cation channels. However, the overall structural architecture and gating mechanisms of Piezo channels have remained unknown. Here we determine the cryo-electron microscopy structure of the full-length (2,547 amino acids) mouse Piezo1 (Piezo1) at a resolution of 4.8 Å. Piezo1 forms a trimeric propeller-like structure (about 900 kilodalton), with the extracellular domains resembling three distal blades and a central cap. The transmembrane region has 14 apparently resolved segments per subunit. These segments form three peripheral wings and a central pore module that encloses a potential ion-conducting pore. The rather flexible extracellular blade domains are connected to the central intracellular domain by three long beam-like structures. This trimeric architecture suggests that Piezo1 may use its peripheral regions as force sensors to gate the central ion-conducting pore.
History
DepositionJun 5, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2015Group: Database references
Revision 1.2Dec 18, 2019Group: Data collection / Database references
Category: database_2 / em_image_scans ...database_2 / em_image_scans / em_software / struct_ref_seq_dif
Item: _em_software.image_processing_id / _em_software.name / _struct_ref_seq_dif.details
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _pdbx_entry_details.has_protein_modification

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Structure visualization

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Assembly

Deposited unit
A: Piezo-type mechanosensitive ion channel component 1
B: Piezo-type mechanosensitive ion channel component 1
C: Piezo-type mechanosensitive ion channel component 1


Theoretical massNumber of molelcules
Total (without water)704,5023
Polymers704,5023
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Piezo-type mechanosensitive ion channel component 1 / Protein FAM38A


Mass: 234834.109 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Piezo1, Fam38a / Production host: Homo sapiens (human) / References: UniProt: E2JF22
Has protein modificationY
Sequence detailsTHE COMPLETE SEQUENCE OF THE PROTEIN IS BASED ON THE ENTIRE SEQUNCE OF UNIPROTKB E2JF22 (PIEZ1_ ...THE COMPLETE SEQUENCE OF THE PROTEIN IS BASED ON THE ENTIRE SEQUNCE OF UNIPROTKB E2JF22 (PIEZ1_MOUSE), WITH C-TERMINAL EXPRESSION TAGS LEVLFQ (MEPHVLGAGLYWLLLPCTLLAASLLRFNALSLVYLLFLLLLPWLPGPSRHSIPGHTGRLLR ALLCLSLLFLVAHLAFQICLHTVPHLDQFLGQNGSLWVKVSQHIGVTRLDLKDIFNTTRLV APDLGVLLASSLCLGLCGRLTRKAGQSRRTQELQDDDDDDDDDDEDIDAAPAVGLKGAPAL ATKRRLWLASRFRVTAHWLLMTSGRTLVIVLLALAGIAHPSAFSSIYLVVFLAICTWWSCH FPLSPLGFNTLCVMVSCFGAGHLICLYCYQTPFIQDMLPPGNIWARLFGLKNFVDLPNYSS PNALVLNTKHAWPIYVSPGILLLLYYTATSLLKLHKSCPSELRKETPREDEEHELELDHLE PEPQARDATQGEMPMTTEPDLDNCTVHVLTSQSPVRQRPVRPRLAELKEMSPLHGLGHLIM DQSYVCALIAMMVWSIMYHSWLTFVLLLWACLIWTVRSRHQLAMLCSPCILLYGLTLCCLR YVWAMELPELPTTLGPVSLHQLGLEHTRYPCLDLGAMLLYLLTFWLLLRQFVKEKLLKKQK VPAALLEVTVADTEPTQTQTLLRSLGELVTGIYVKYWIYVCAGMFIVVSFAGRLVVYKIVY MFLFLLCLTLFQVYYTLWRKLLRVFWWLVVAYTMLVLIAVYTFQFQDFPTYWRNLTGFTDE QLGDLGLEQFSVSELFSSILIPGFFLLACILQLHYFHRPFMQLTDLEHVPPPGTRHPRWAH RQDAVSEAPLLEHQEEEEVFREDGQSMDGPHQATQVPEGTASKWGLVADRLLDLAASFSAV LTRIQVFVRRLLELHVFKLVALYTVWVALKEVSVMNLLLVVLWAFALPYPRFRPMASCLST VWTCIIIVCKMLYQLKIVNPHEYSSNCTEPFPNNTNLQPLEINQSLLYRGPVDPANWFGVR KGYPNLGYIQNHLQILLLLVFEAVVYRRQEHYRRQHQQAPLPAQAVCADGTRQRLDQDLLS CLKYFINFFFYKFGLEICFLMAVNVIGQRMNFMVILHGCWLVAILTRRRREAIARLWPNYC LFLTLFLLYQYLLCLGMPPALCIDYPWRWSKAIPMNSALIKWLYLPDFFRAPNSTNLISDF LLLLCASQQWQVFSAERTEEWQRMAGINTDHLEPLRGEPNPIPNFIHCRSYLDMLKVAVFR YLFWLVLVVVFVAGATRISIFGLGYLLACFYLLLFGTTLLQKDTRAQLVLWDCLILYNVTV IISKNMLSLLSCVFVEQMQSNFCWVIQLFSLVCTVKGYYDPKEMMTRDRDCLLPVEEAGII WDSICFFFLLLQRRIFLSHYFLHVSADLKATALQASRGFALYNAANLKSINFHRQIEEKSL AQLKRQMKRIRAKQEKYRQSQASRGQLQSKDPQDPSQEPGPDSPGGSSPPRRQWWRPWLDH ATVIHSGDYFLFESDSEEEEEALPEDPRPAAQSAFQMAYQAWVTNAQTVLRQRRERARQER AEQLASGGDLNPDVEPVDVPEDEMAGRSHMMQRVLSTMQFLWVLGQATVDGLTRWLRAFTK HHRTMSDVLCAERYLLTQELLRVGEVRRGVLDQLYVGEDEATLSGPVETRDGPSTASSGLG AEEPLSSMTDDTSSPLSTGYNTRSGSEEIVTDAGDLQAGTSLHGSQELLANARTRMRTASE LLLDRRLHIPELEEAERFEAQQGRTLRLLRAGYQCVAAHSELLCYFIIILNHMVTASAASL VLPVLVFLWAMLTIPRPSKRFWMTAIVFTEVMVVTKYLFQFGFFPWNSYVVLRRYENKPYF PPRILGLEKTDSYIKYDLVQLMALFFHRSQLLCYGLWDHEEDRYPKDHCRSSVKDREAKEE PEAKLESQSETGTGHPKEPVLAGTPRDHIQGKGSIRSKDVIQDPPEDLKPRHTRHISIRFR RRKETPGPKGTAVMETEHEEGEGKETTERKRPRHTQEKSKFRERMKAAGRRLQSFCVSLAQ SFYQPLQRFFHDILHTKYRAATDVYALMFLADIVDIIIIIFGFWAFGKHSAATDIASSLSD DQVPQAFLFMLLVQFGTMVIDRALYLRKTVLGKLAFQVVLVVAIHIWMFFILPAVTERMFS QNAVAQLWYFVKCIYFALSAYQIRCGYPTRILGNFLTKKYNHLNLFLFQGFRLVPFLVELR AVMDWVWTDTTLSLSNWMCVEDIYANIFIIKCSRETEKKYPQPKGQKKKKIVKYGMGGLII LFLIAIIWFPLLFMSLIRSVVGVVNQPIDVTVTLKLGGYEPLFTMSAQQPSIVPFTPQAYE ELSQQFDPYPLAMQFISQYSPEDIVTAQIEGSSGALWRISPPSRAQMKQELYNGTADITLR FTWNFQRDLAKGGTVEYTNEKHTLELAPNSTARRQLAQLLEGRPDQSVVIPHLFPKYIRAP NGPEANPVKQLQPDEEEDYLGVRIQLRREQVGTGASGEQAGTKASDFLEWWVIELQDCKAD CNLLPMVIFSDKVSPPSLGFLAGYGIVGLYVSIVLVVGKFVRGFFSEISHSIMFEELPCVD RILKLCQDIFLVRETRELELEEELYAKLIFLYRSPETMIKWTRERELEVLFQ). AUTHORS ARE NOT SURE OF THE EXACT POSITION OF THE RESIDUES EXCEPT FOR RESIDUES 2218-2456 OF WHICH A CRYSTAL STRUCTURE HAS BEEN SOLVED. RESIDUES 1961-2217 WERE NUMBERED AND PLACED BASED ON THE DENSITY MAP, SEQUENCE ANALYSIS AND SOME FUNCTIONAL EXPERIMENT.

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: channel / Type: COMPLEX
Molecular weightValue: 0.9 MDa / Experimental value: NO
Buffer solutionpH: 7.2
Details: 25 mM NaPIPES, 140 mM NaCl, 2 mM DTT and 0.026% (w/v) C12E10
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: YES / Vitrification applied: YES
Details: 25 mM NaPIPES, 140 mM NaCl, 2 mM DTT and 0.026% (w/v) C12E10 (Stain Details Grids with adsorbed protein floated on 2% w/v uranyl acetate for 30 seconds)
EM stainingType: NEGATIVE / Material: Uranyl Acetate
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Apr 25, 2014
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 22500 X / Camera length: 0 mm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 16 e/Å2 / Film or detector model: GATAN K2 (4k x 4k)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM softwareName: RELION / Category: 3D reconstruction
CTF correctionDetails: CTFFIND
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 30021 / Details: (Single particle--Applied symmetry: C3) / Symmetry type: POINT
Atomic model buildingPDB-ID: 4RAX

4rax


Accession code: 4RAX / Source name: PDB / Type: experimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms15741 0 0 0 15741

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