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- EMDB-39219: Human PIEZO1-A1988V-MDFIC -

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Basic information

Entry
Database: EMDB / ID: EMD-39219
TitleHuman PIEZO1-A1988V-MDFIC
Map data
Sample
  • Complex: Human PIEZO1-A1988V-MDFIC
    • Protein or peptide: Piezo-type mechanosensitive ion channel component 1
    • Protein or peptide: MyoD family inhibitor domain-containing protein
  • Ligand: DODECANE
  • 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 / positive regulation of viral transcription / 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 / Tat protein binding / stereocilium / regulation of Wnt signaling pathway ...mechanosensitive monoatomic cation channel activity / positive regulation of viral transcription / 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 / Tat protein binding / stereocilium / regulation of Wnt signaling pathway / regulation of JNK cascade / Mechanical load activates signaling by PIEZO1 and integrins in osteocytes / negative regulation of protein import into nucleus / positive regulation of myotube differentiation / lamellipodium membrane / monoatomic cation transport / monoatomic cation channel activity / endoplasmic reticulum-Golgi intermediate compartment membrane / cyclin binding / 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 / DNA-binding transcription factor binding / negative regulation of DNA-templated transcription / endoplasmic reticulum membrane / positive regulation of DNA-templated transcription / nucleolus / endoplasmic reticulum / extracellular region / nucleus / plasma membrane / cytoplasm
Similarity search - Function
MyoD family inhibitor/MyoD family inhibitor domain-containing protein / MyoD family inhibitor / 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
Similarity search - Domain/homology
Piezo-type mechanosensitive ion channel component 1 / MyoD family inhibitor domain-containing protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsZhang MF
Funding support China, 1 items
OrganizationGrant numberCountry
Other government China
CitationJournal: 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
DepositionFeb 24, 2024-
Header (metadata) releaseJan 15, 2025-
Map releaseJan 15, 2025-
UpdateJan 15, 2025-
Current statusJan 15, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39219.png

Downloads & links

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Map

FileDownload / File: emd_39219.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.57 Å/pix.
x 800 pix.
= 456. Å		0.57 Å/pix.
x 800 pix.
= 456. Å		0.57 Å/pix.
x 800 pix.
= 456. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.57 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.22678392 - 0.38496482
Average (Standard dev.)0.000010198738 (±0.0073421984)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions800800800
Spacing800800800
CellA=B=C: 456.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_39219_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_39219_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human PIEZO1-A1988V-MDFIC

EntireName: Human PIEZO1-A1988V-MDFIC
Components
  • Complex: Human PIEZO1-A1988V-MDFIC
    • Protein or peptide: Piezo-type mechanosensitive ion channel component 1
    • Protein or peptide: MyoD family inhibitor domain-containing protein
  • Ligand: DODECANE
  • Ligand: (1S)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(octadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate

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Supramolecule #1: Human PIEZO1-A1988V-MDFIC

SupramoleculeName: Human PIEZO1-A1988V-MDFIC / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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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: Homo sapiens (human)
Molecular weightTheoretical: 287.094062 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEPHVLGAVL YWLLLPCALL AACLLRFSGL SLVYLLFLLL LPWFPGPTRC GLQGHTGRLL RALLGLSLLF LVAHLALQIC LHIVPRLDQ LLGPSCSRWE TLSRHIGVTR LDLKDIPNAI RLVAPDLGIL VVSSVCLGIC GRLARNTRQS PHPRELDDDE R DVDASPTA ...String:
MEPHVLGAVL YWLLLPCALL AACLLRFSGL SLVYLLFLLL LPWFPGPTRC GLQGHTGRLL RALLGLSLLF LVAHLALQIC LHIVPRLDQ LLGPSCSRWE TLSRHIGVTR LDLKDIPNAI RLVAPDLGIL VVSSVCLGIC GRLARNTRQS PHPRELDDDE R DVDASPTA GLQEAATLAP TRRSRLAARF RVTAHWLLVA AGRVLAVTLL ALAGIAHPSA LSSVYLLLFL ALCTWWACHF PI STRGFSR LCVAVGCFGA GHLICLYCYQ MPLAQALLPP AGIWARVLGL KDFVGPTNCS SPHALVLNTG LDWPVYASPG VLL LLCYAT ASLRKLRAYR PSGQRKEAAK GYEARELELA ELDQWPQERE SDQHVVPTAP DTEADNCIVH ELTGQSSVLR RPVR PKRAE PREASPLHSL GHLIMDQSYV CALIAMMVWS ITYHSWLTFV LLLWACLIWT VRSRHQLAML CSPCILLYGM TLCCL RYVW AMDLRPELPT TLGPVSLRQL GLEHTRYPCL DLGAMLLYTL TFWLLLRQFV KEKLLKWAES PAALTEVTVA DTEPTR TQT LLQSLGELVK GVYAKYWIYV CAGMFIVVSF AGRLVVYKIV YMFLFLLCLT LFQVYYSLWR KLLKAFWWLV VAYTMLV LI AVYTFQFQDF PAYWRNLTGF TDEQLGDLGL EQFSVSELFS SILVPGFFLL ACILQLHYFH RPFMQLTDME HVSLPGTR L PRWAHRQDAV SGTPLLREEQ QEHQQQQQEE EEEEEDSRDE GLGVATPHQA TQVPEGAAKW GLVAERLLEL AAGFSDVLS RVQVFLRRLL ELHVFKLVAL YTVWVALKEV SVMNLLLVVL WAFALPYPRF RPMASCLSTV WTCVIIVCKM LYQLKVVNPQ EYSSNCTEP FPNSTNLLPT EISQSLLYRG PVDPANWFGV RKGFPNLGYI QNHLQVLLLL VFEAIVYRRQ EHYRRQHQLA P LPAQAVFA SGTRQQLDQD LLGCLKYFIN FFFYKFGLEI CFLMAVNVIG QRMNFLVTLH GCWLVAILTR RHRQAIARLW PN YCLFLAL FLLYQYLLCL GMPPALCIDY PWRWSRAVPM NSALIKWLYL PDFFRAPNST NLISDFLLLL CASQQWQVFS AER TEEWQR MAGVNTDRLE PLRGEPNPVP NFIHCRSYLD MLKVAVFRYL FWLVLVVVFV TGATRISIFG LGYLLACFYL LLFG TALLQ RDTRARLVLW DCLILYNVTV IISKNMLSLL ACVFVEQMQT GFCWVIQLFS LVCTVKGYYD PKEMMDRDQD CLLPV EEAG IIWDSVCFFF LLLQRRVFLS HYYLHVRADL QATALLASRG FALYNAANLK SIDFHRRIEE KSLAQLKRQM ERIRAK QEK HRQGRVDRSR PQDTLGPKDP GLEPGPDSPG GSSPPRRQWW RPWLDHATVI HSGDYFLFES DSEEEEEAVP EDPRPSA QS AFQLAYQAWV TNAQAVLRRR QQEQEQARQE QAGQLPTGGG PSQEVEPAEG PEEAAAGRSH VVQRVLSTAQ FLWMLGQA L VDELTRWLQE FTRHHGTMSD VLRAERYLLT QELLQGGEVH RGVLDQLYTS QAEATLPGPT EAPNAPSTVS SGLGAEEPL SSMTDDMGSP LSTGYHTRSG SEEAVTDPGE REAGASLYQG LMRTASELLL DRRLRIPELE EAELFAEGQG RALRLLRAVY QCVAAHSEL LCYFIIILNH MVTASAGSLV LPVLVFLWAM LSIPRPSKRF WMTAIVFTEI AVVVKYLFQF GFFPWNSHVV L RRYENKPY FPPRILGLEK TDGYIKYDLV QLMALFFHRS QLLCYGLWDH EEDSPSKEHD KSGEEEQGAE EGPGVPAATT ED HIQVEAR VGPTDGTPEP QVELRPRDTR RISLRFRRRK KEGPARKGAA AIEAEDREEE EGEEEKEAPT GREKRPSRSG GRV RAAGRR LQGFCLSLAQ GTYRPLRRFF HDILHTKYRA ATDVYALMFL ADVVDFIIII FGFWAFGKHS AATDITSSLS DDQV PEAFL VMLLIQFSTM VVDRALYLRK TVLGKLAFQV ALVLAIHLWM FFILPAVTER MFNQNVVAQL WYFVKCIYFA LSAYQ IRCG YPTRILGNFL TKKYNHLNLF LFQGFRLVPF LVELRAVMDW VWTDTTLSLS SWMCVEDIYA NIFIIKCSRE TEKKYP QPK GQKKKKIVKY GMGGLIILFL IAIIWFPLLF MSLVRSVVGV VNQPIDVTVT LKLGGYEPLF TMSAQQPSII PFTAQAY EE LSRQFDPQPL AMQFISQYSP EDIVTAQIEG SSGALWRISP PSRAQMKREL YNGTADITLR FTWNFQRDLA KGGTVEYA N EKHMLALAPN STARRQLASL LEGTSDQSVV IPNLFPKYIR APNGPEANPV KQLQPNEEAD YLGVRIQLRR EQGAGATGF LEWWVIELQE CRTDCNLLPM VIFSDKVSPP SLGFLAGYGI MGLYVSIVLV IGKFVRGFFS EISHSIMFEE LPCVDRILKL CQDIFLVRE TRELELEEEL YAKLIFLYRS PETMIKWTRE KE

UniProtKB: Piezo-type mechanosensitive ion channel component 1

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Macromolecule #2: MyoD family inhibitor domain-containing protein

MacromoleculeName: MyoD family inhibitor domain-containing protein / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.814113 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSGAGEALAP GPVGPQRVAE AGGGQLGSTA QGKCDKDNTE KDITQATNSH FTHGEMQDQS IWGNPSDGEL IRTQPQRLPQ LQTSAQVPS GEEIGKIKNG HTGLSNGNGI HHGAKHGSAD NRKLSAPVSQ KMHRKIQSSL SVNSDISKKS KVNAVFSQKT G SSPEDCCV ...String:
MSGAGEALAP GPVGPQRVAE AGGGQLGSTA QGKCDKDNTE KDITQATNSH FTHGEMQDQS IWGNPSDGEL IRTQPQRLPQ LQTSAQVPS GEEIGKIKNG HTGLSNGNGI HHGAKHGSAD NRKLSAPVSQ KMHRKIQSSL SVNSDISKKS KVNAVFSQKT G SSPEDCCV HCILACLFCE FLTLCNIVLG QASCGICTSE ACCCCCGDEM GDDCNCPCDM DCGIMDACCE SSDCLEICME CC GICFPS

UniProtKB: MyoD family inhibitor domain-containing protein

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Macromolecule #3: DODECANE

MacromoleculeName: DODECANE / type: ligand / ID: 3 / Number of copies: 15 / Formula: D12
Molecular weightTheoretical: 170.335 Da
Chemical component information

ChemComp-D12:
DODECANE

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Macromolecule #4: (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: 4 / 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

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI 10
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 40207
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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