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- PDB-9vmx: Human PIEZO1-E756del-MDFIC -

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Basic information

Entry
Database: PDB / ID: 9vmx
TitleHuman PIEZO1-E756del-MDFIC
Components
  • MyoD family inhibitor domain-containing protein
  • Piezo-type mechanosensitive ion channel component 1
KeywordsMEMBRANE PROTEIN / Complex of human PIEZO1-E756del and MDFIC
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 ...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
DODECANE / Chem-L9Q / Piezo-type mechanosensitive ion channel component 1 / MyoD family inhibitor domain-containing protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsZhang, M.F. / Pei, D.Q.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)92068201 China
Other government2024SSYS0031
CitationJournal: To Be Published
Title: Structure of human PIEZO1 and its slow inactivating channelopathy mutants
Authors: Pei, D.Q. / Zhang, M.F.
History
DepositionJun 29, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release
Revision 1.0Jul 16, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 16, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 16, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 16, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 16, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 16, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jul 16, 2025Data 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
B: Piezo-type mechanosensitive ion channel component 1
D: Piezo-type mechanosensitive ion channel component 1
C: MyoD family inhibitor domain-containing protein
E: MyoD family inhibitor domain-containing protein
F: MyoD family inhibitor domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)943,51824
Polymers938,7256
Non-polymers4,79318
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 / Membrane protein induced by beta-amyloid treatment / Mib / Protein FAM38A


Mass: 287094.062 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIEZO1, FAM38A, KIAA0233 / Production host: Homo sapiens (human) / References: UniProt: Q92508
#2: Protein MyoD family inhibitor domain-containing protein / I-mfa domain-containing protein / hIC


Mass: 25814.113 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MDFIC / Production host: Homo sapiens (human) / References: UniProt: Q9P1T7
#3: Chemical
ChemComp-D12 / DODECANE


Mass: 170.335 Da / Num. of mol.: 15
Source method: isolated from a genetically manipulated source
Formula: C12H26
#4: Chemical ChemComp-L9Q / (1S)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(octadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate / 1-stearoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine


Mass: 746.050 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C41H80NO8P
Has ligand of interestN
Has protein modificationY

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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: Complex of hPIEZO1-E756del and MDFIC / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
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: 1300 nm / Nominal defocus min: 900 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 40207 / Symmetry type: POINT

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