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- EMDB-35577: Cryo-EM structure of mouse Piezo1-MDFIC complex (composite map) -

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Basic information

Entry
Database: EMDB / ID: EMD-35577
TitleCryo-EM structure of mouse Piezo1-MDFIC complex (composite map)
Map dataCryo-EM structure of mouse Piezo1-MDFIC complex (composite map)
Sample
  • Complex: Piezo1 in complex with MDFIC
    • Protein or peptide: Piezo-type mechanosensitive ion channel component 1
    • Protein or peptide: MyoD family inhibitor domain-containing protein
KeywordsPiezo1 complex / mechanosensation / mechanotransduction / MEMBRANE PROTEIN
Function / homology
Function and homology information


mechanosensitive monoatomic cation channel activity / positive regulation of viral transcription / positive regulation of cell-cell adhesion mediated by integrin / detection of mechanical stimulus / mechanosensitive monoatomic ion channel activity / positive regulation of integrin activation / Tat protein binding / regulation of Wnt signaling pathway / negative regulation of protein import into nucleus / positive regulation of myotube differentiation ...mechanosensitive monoatomic cation channel activity / positive regulation of viral transcription / positive regulation of cell-cell adhesion mediated by integrin / detection of mechanical stimulus / mechanosensitive monoatomic ion channel activity / positive regulation of integrin activation / Tat protein binding / regulation of Wnt signaling pathway / negative regulation of protein import into nucleus / positive regulation of myotube differentiation / lamellipodium membrane / monoatomic cation transport / regulation of JNK cascade / monoatomic cation channel activity / regulation of membrane potential / endoplasmic reticulum-Golgi intermediate compartment membrane / cyclin binding / cellular response to mechanical stimulus / DNA-binding transcription factor binding / negative regulation of DNA-templated transcription / endoplasmic reticulum membrane / nucleolus / positive regulation of DNA-templated transcription / endoplasmic reticulum / extracellular region / identical protein binding / 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, R-Ras-binding domain / Piezo
Similarity search - Domain/homology
Piezo-type mechanosensitive ion channel component 1 / MyoD family inhibitor domain-containing protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.66 Å
AuthorsZhou Z / Ma X / Lin Y / Cheng D / Bavi N / Li JV / Sutton D / Yao M / Harvey N / Corry B ...Zhou Z / Ma X / Lin Y / Cheng D / Bavi N / Li JV / Sutton D / Yao M / Harvey N / Corry B / Zhang Y / Cox CD
Funding support Australia, China, 2 items
OrganizationGrant numberCountry
Australian Research Council (ARC)FT220100159 Australia
Ministry of Science and Technology (MoST, China)STI2030-7400 China
CitationJournal: Science / Year: 2023
Title: MyoD-family inhibitor proteins act as auxiliary subunits of Piezo channels.
Authors: Zijing Zhou / Xiaonuo Ma / Yiechang Lin / Delfine Cheng / Navid Bavi / Genevieve A Secker / Jinyuan Vero Li / Vaibhao Janbandhu / Drew L Sutton / Hamish S Scott / Mingxi Yao / Richard P ...Authors: Zijing Zhou / Xiaonuo Ma / Yiechang Lin / Delfine Cheng / Navid Bavi / Genevieve A Secker / Jinyuan Vero Li / Vaibhao Janbandhu / Drew L Sutton / Hamish S Scott / Mingxi Yao / Richard P Harvey / Natasha L Harvey / Ben Corry / Yixiao Zhang / Charles D Cox /
Abstract: Piezo channels are critical cellular sensors of mechanical forces. Despite their large size, ubiquitous expression, and irreplaceable roles in an ever-growing list of physiological processes, few ...Piezo channels are critical cellular sensors of mechanical forces. Despite their large size, ubiquitous expression, and irreplaceable roles in an ever-growing list of physiological processes, few Piezo channel-binding proteins have emerged. In this work, we found that MyoD (myoblast determination)-family inhibitor proteins (MDFIC and MDFI) are PIEZO1/2 interacting partners. These transcriptional regulators bind to PIEZO1/2 channels, regulating channel inactivation. Using single-particle cryogenic electron microscopy, we mapped the interaction site in MDFIC to a lipidated, C-terminal helix that inserts laterally into the PIEZO1 pore module. These Piezo-interacting proteins fit all the criteria for auxiliary subunits, contribute to explaining the vastly different gating kinetics of endogenous Piezo channels observed in many cell types, and elucidate mechanisms potentially involved in human lymphatic vascular disease.
History
DepositionMar 7, 2023-
Header (metadata) releaseAug 9, 2023-
Map releaseAug 9, 2023-
UpdateAug 30, 2023-
Current statusAug 30, 2023Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_35577.png

Downloads & links

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Map

FileDownload / File: emd_35577.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of mouse Piezo1-MDFIC complex (composite map)
Voxel sizeX=Y=Z: 1.055 Å
Density
Contour LevelBy AUTHOR: 1.3
Minimum - Maximum-4.7183285 - 9.164396
Average (Standard dev.)0.023894839 (±0.16849346)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 421.99997 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Local refinement of the transmembrane domain

Fileemd_35577_additional_1.map
AnnotationLocal refinement of the transmembrane domain
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Local refinement of the cap domain

Fileemd_35577_additional_2.map
AnnotationLocal refinement of the cap domain
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: The consensus map without local masked refinement

Fileemd_35577_additional_3.map
AnnotationThe consensus map without local masked refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Piezo1 in complex with MDFIC

EntireName: Piezo1 in complex with MDFIC
Components
  • Complex: Piezo1 in complex with MDFIC
    • Protein or peptide: Piezo-type mechanosensitive ion channel component 1
    • Protein or peptide: MyoD family inhibitor domain-containing protein

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Supramolecule #1: Piezo1 in complex with MDFIC

SupramoleculeName: Piezo1 in complex with MDFIC / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse)

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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

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: Mus musculus (house mouse)
Molecular weightTheoretical: 26.122732 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSCAGEALAP GPAEQQCPVE AGGGRLGSPA HEACNEDNTE KDKRPATSGH TRCGLMRDQS IWPNPSAGEL VRTQPERLPQ LQTSAQEPG KEETGKIKNG GHTRMSNGNG IPHGAKHVSV ENHKISAPVS QKMHRKIQSS LSVNNDISKK SKVNAVFSPK A ASSPEDCC ...String:
MSCAGEALAP GPAEQQCPVE AGGGRLGSPA HEACNEDNTE KDKRPATSGH TRCGLMRDQS IWPNPSAGEL VRTQPERLPQ LQTSAQEPG KEETGKIKNG GHTRMSNGNG IPHGAKHVSV ENHKISAPVS QKMHRKIQSS LSVNNDISKK SKVNAVFSPK A ASSPEDCC VHCILACLFC EFLTLCNIVL GQASCGICTS EACCCCCGDE MGDDCSCPCD MDCGIMDACC ESSDCLEICM EC CGICFPS

UniProtKB: MyoD family inhibitor domain-containing protein

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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: 7.9
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.2 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 49.4 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.66 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 102644

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