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- EMDB-64998: The cryo-EM structure of mouse Piezo1-MDFI complex -

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Basic information

Entry
Database: EMDB / ID: EMD-64998
TitleThe cryo-EM structure of mouse Piezo1-MDFI complex
Map dataresample on EMD-35577
Sample
  • Complex: The cryo-EM structure of mouse Piezo1-MDFI complex
    • Protein or peptide: Piezo-type mechanosensitive ion channel component 1,Green fluorescent protein
    • Protein or peptide: Isoform I-mfA of MyoD family inhibitor
KeywordsPiezo1 / mechanosensitive channel / MDFI / MEMBRANE PROTEIN
Function / homology
Function and homology information


mechanosensitive monoatomic cation channel activity / cuticular plate / trophoblast giant cell differentiation / embryonic skeletal system morphogenesis / dorsal/ventral axis specification / maintenance of protein location in cell / positive regulation of integrin activation / positive regulation of cell-cell adhesion mediated by integrin / detection of mechanical stimulus / mechanosensitive monoatomic ion channel activity ...mechanosensitive monoatomic cation channel activity / cuticular plate / trophoblast giant cell differentiation / embryonic skeletal system morphogenesis / dorsal/ventral axis specification / maintenance of protein location in cell / positive regulation of integrin activation / positive regulation of cell-cell adhesion mediated by integrin / detection of mechanical stimulus / mechanosensitive monoatomic ion channel activity / stereocilium / regulation of Wnt signaling pathway / regulation of JNK cascade / positive regulation of myotube differentiation / negative regulation of Wnt signaling pathway / lamellipodium membrane / monoatomic cation transport / monoatomic cation channel activity / endoplasmic reticulum-Golgi intermediate compartment membrane / bioluminescence / generation of precursor metabolites and energy / protein sequestering activity / regulation of membrane potential / cellular response to mechanical stimulus / DNA-binding transcription factor binding / negative regulation of DNA-templated transcription / endoplasmic reticulum membrane / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
MyoD family inhibitor/MyoD family inhibitor domain-containing protein / 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 ...MyoD family inhibitor/MyoD family inhibitor domain-containing protein / 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 / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein
Similarity search - Domain/homology
Piezo-type mechanosensitive ion channel component 1 / Green fluorescent protein / MyoD family inhibitor
Similarity search - Component
Biological speciesMus musculus (house mouse) / Aequorea victoria (jellyfish)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.63 Å
AuthorsZhang Y / Dai F
Funding support China, Australia, 2 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2022ZD0207400 China
Australian Research Council (ARC)FT220100159 Australia
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2026
Title: MDFIC2 is a sensory neuron-specific PIEZO channel auxiliary subunit
Authors: Zhang Y / Dai F
History
DepositionJun 9, 2025-
Header (metadata) releaseApr 8, 2026-
Map releaseApr 8, 2026-
UpdateApr 8, 2026-
Current statusApr 8, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64998.png

Downloads & links

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Map

FileDownload / File: emd_64998.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationresample on EMD-35577
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 380 pix.
= 400.9 Å		1.06 Å/pix.
x 380 pix.
= 400.9 Å		1.06 Å/pix.
x 380 pix.
= 400.9 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.055 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.34
Minimum - Maximum-1.5878367 - 2.8399282
Average (Standard dev.)0.008537338 (±0.056676805)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions380380380
Spacing380380380
CellA=B=C: 400.9 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: resample on EMD-35577

Fileemd_64998_half_map_1.map
Annotationresample on EMD-35577
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: resample on EMD-35577

Fileemd_64998_half_map_2.map
Annotationresample on EMD-35577
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : The cryo-EM structure of mouse Piezo1-MDFI complex

EntireName: The cryo-EM structure of mouse Piezo1-MDFI complex
Components
  • Complex: The cryo-EM structure of mouse Piezo1-MDFI complex
    • Protein or peptide: Piezo-type mechanosensitive ion channel component 1,Green fluorescent protein
    • Protein or peptide: Isoform I-mfA of MyoD family inhibitor

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Supramolecule #1: The cryo-EM structure of mouse Piezo1-MDFI complex

SupramoleculeName: The cryo-EM structure of mouse Piezo1-MDFI complex / 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,Green fluores...

MacromoleculeName: Piezo-type mechanosensitive ion channel component 1,Green fluorescent protein
type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Aequorea victoria (jellyfish)
Molecular weightTheoretical: 322.403781 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 IKWTRERESN SLEVLFQGPT A AAAVSKGE ELFTGVVPIL VELDGDVNGH KFSVSGEGEG DATYGKLTLK FICTTGKLPV PWPTLVTTLT YGVQCFSRYP DH MKQHDFF KSAMPEGYVQ ERTIFFKDDG NYKTRAEVKF EGDTLVNRIE LKGIDFKEDG NILGHKLEYN YNSHNVYIMA DKQ KNGIKV NFKIRHNIED GSVQLADHYQ QNTPIGDGPV LLPDNHYLST QSKLSKDPNE KRDHMVLLEF VTAAGITLGM DELY KSGGG HHHHHHHHHH

UniProtKB: Piezo-type mechanosensitive ion channel component 1, Green fluorescent protein

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Macromolecule #2: Isoform I-mfA of MyoD family inhibitor

MacromoleculeName: Isoform I-mfA of MyoD family inhibitor / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 27.539625 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYKDDDDKG GGGSSTTNGS SATMSQVSGQ CPSRCDAPHG VPSAALDPAQ TMSLLPGLEV ARSTHPVEAS SEEGFPEEAA PSMPHDSGL RAQQALNSID LDVPTEAVTC QPQGNPQGCT PLLPNGSSHD HLSEPGSAGH AGNGALGGSK AHRKLQTHPS L GSQAGRKS ...String:
MDYKDDDDKG GGGSSTTNGS SATMSQVSGQ CPSRCDAPHG VPSAALDPAQ TMSLLPGLEV ARSTHPVEAS SEEGFPEEAA PSMPHDSGL RAQQALNSID LDVPTEAVTC QPQGNPQGCT PLLPNGSSHD HLSEPGSAGH AGNGALGGSK AHRKLQTHPS L GSQAGRKS RGSARSASQV PLQAQEDCCV HCILSCLFCE FLTLCNILLD CATCGSCSSE DSCLCCCCCG SGECADCDLP CD LDCGIVD ACCESADCLE ICMECCGLCF SS

UniProtKB: MyoD family inhibitor

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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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 49.41 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.4000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8imz

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.63 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 56377
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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