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- PDB-9ved: The cryo-EM structure of mouse Piezo1-MDFI complex -

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Basic information

Entry
Database: PDB / ID: 9ved
TitleThe cryo-EM structure of mouse Piezo1-MDFI complex
Components
  • Isoform I-mfA of MyoD family inhibitor
  • Piezo-type mechanosensitive ion channel component 1,Green fluorescent protein
KeywordsMEMBRANE PROTEIN / Piezo1 / mechanosensitive channel / MDFI
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.63 Å
AuthorsZhang, Y. / Dai, F.
Funding support China, Australia, 2items
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, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 8, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Piezo-type mechanosensitive ion channel component 1,Green fluorescent protein
C: Piezo-type mechanosensitive ion channel component 1,Green fluorescent protein
B: Piezo-type mechanosensitive ion channel component 1,Green fluorescent protein
F: Isoform I-mfA of MyoD family inhibitor
D: Isoform I-mfA of MyoD family inhibitor
E: Isoform I-mfA of MyoD family inhibitor


Theoretical massNumber of molelcules
Total (without water)1,049,8306
Polymers1,049,8306
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Piezo-type mechanosensitive ion channel component 1,Green fluorescent protein / Protein FAM38A


Mass: 322403.781 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Aequorea victoria (jellyfish)
Gene: Piezo1, Fam38a, GFP / Production host: Homo sapiens (human) / References: UniProt: E2JF22, UniProt: P42212
#2: Protein Isoform I-mfA of MyoD family inhibitor / Myogenic repressor I-mf


Mass: 27539.625 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mdfi / Production host: Homo sapiens (human) / References: UniProt: P70331
Has protein modificationN

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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: The cryo-EM structure of mouse Piezo1-MDFI complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Mus musculus (house mouse)10090
31Aequorea victoria (jellyfish)6100
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.9
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 1400 nm
Image recordingElectron dose: 49.41 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELIONparticle selection
2PHENIX1.18.2_3874model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 3.63 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 56377 / Symmetry type: POINT
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01230075
ELECTRON MICROSCOPYf_angle_d0.96140800
ELECTRON MICROSCOPYf_dihedral_angle_d24.3884026
ELECTRON MICROSCOPYf_chiral_restr0.0534683
ELECTRON MICROSCOPYf_plane_restr0.0065088

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