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- PDB-8imz: Cryo-EM structure of mouse Piezo1-MDFIC complex (composite map) -

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Basic information

Entry
Database: PDB / ID: 8imz
TitleCryo-EM structure of mouse Piezo1-MDFIC complex (composite map)
Components
  • MyoD family inhibitor domain-containing protein
  • Piezo-type mechanosensitive ion channel component 1
KeywordsMEMBRANE PROTEIN / Piezo1 complex / mechanosensation / mechanotransduction
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 / stereocilium / Tat protein binding / 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 / stereocilium / Tat protein binding / regulation of Wnt signaling pathway / regulation of JNK cascade / 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 / regulation of membrane potential / 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 / 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, cap domain / Piezo TM25-28 ...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 / Piezo TM1-24 / Piezo, THU9 and anchor domain
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.66 Å
AuthorsZhou, Z. / Ma, X. / Lin, Y. / Cheng, D. / Bavi, N. / Li, J.V. / Sutton, D. / Yao, M. / Harvey, N. / Corry, B. ...Zhou, Z. / Ma, X. / Lin, Y. / Cheng, D. / Bavi, N. / Li, J.V. / Sutton, D. / Yao, M. / Harvey, N. / Corry, B. / Zhang, Y. / Cox, C.D.
Funding support Australia, China, 2items
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, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 9, 2023Provider: repository / Type: Initial release
Revision 1.0Aug 9, 2023Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 9, 2023Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Aug 9, 2023Data content type: Additional map / Part number: 2 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Aug 9, 2023Data content type: Additional map / Part number: 3 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Aug 9, 2023Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 9, 2023Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Aug 9, 2023Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Aug 9, 2023Data content type: Additional map / Part number: 2 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Aug 9, 2023Data content type: Additional map / Part number: 3 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Aug 9, 2023Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 9, 2023Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 23, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jul 23, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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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
D: MyoD family inhibitor domain-containing protein
E: MyoD family inhibitor domain-containing protein
C: Piezo-type mechanosensitive ion channel component 1
B: Piezo-type mechanosensitive ion channel component 1
F: MyoD family inhibitor domain-containing protein


Theoretical massNumber of molelcules
Total (without water)955,3306
Polymers955,3306
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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


Mass: 292320.656 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
#2: Protein MyoD family inhibitor domain-containing protein / I-mfa domain-containing protein / Kidney cell line-derived transcript 1


Mass: 26122.732 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mdfic, Kdt1 / Production host: Homo sapiens (human) / References: UniProt: Q8BX65
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: Piezo1 in complex with MDFIC / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Source (natural)Organism: Mus musculus (house mouse)
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: FEI TITAN 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: 1200 nm
Image recordingElectron dose: 49.4 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.66 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 102644 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00730084
ELECTRON MICROSCOPYf_angle_d0.73840815
ELECTRON MICROSCOPYf_dihedral_angle_d24.6364026
ELECTRON MICROSCOPYf_chiral_restr0.0464683
ELECTRON MICROSCOPYf_plane_restr0.0055091

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