8ZU3 | pdb_00008zu3

Human PIEZO1-MDFIC


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of human PIEZO1 and its slow-inactivating channelopathy mutants.

Shan, Y.Guo, X.Zhang, M.Chen, M.Li, Y.Zhang, M.Pei, D.

(2025) Elife 13

  • DOI: https://doi.org/10.7554/eLife.101923
  • Primary Citation of Related Structures:  
    8YEZ, 8YFC, 8YFG, 8ZU3, 8ZU8

  • PubMed Abstract: 

    PIEZO channels transmit mechanical force signals to cells, allowing them to make critical decisions during development and in pathophysiological conditions. Their fast/slow inactivation modes have been implicated in mechanopathologies but remain poorly understood. Here, we report several near-atomic resolution cryo-EM structures of fast-inactivating wild-type human PIEZO1 (hPIEZO1) and its slow-inactivating channelopathy mutants with or without its auxiliary subunit MDFIC. Our results suggest that hPIEZO1 has a more flattened and extended architecture than curved mouse PIEZO1 (mPIEZO1). The multi-lipidated MDFIC subunits insert laterally into the hPIEZO1 pore module like mPIEZO1, resulting in a more curved and extended state. Interestingly, the high-resolution structures suggest that the pore lipids, which directly seal the central hydrophobic pore, may be involved in the rapid inactivation of hPIEZO1. While the severe hereditary erythrocytosis mutant R2456H significantly slows down the inactivation of hPIEZO1, the hPIEZO1-R2456H-MDFIC complex shows a more curved and contracted structure with an inner helix twist due to the broken link between the pore lipid and R2456H. These results suggest that the pore lipids may be involved in the mechanopathological rapid inactivation mechanism of PIEZO channels.


  • Organizational Affiliation
    • Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Piezo-type mechanosensitive ion channel component 1A,
B,
C [auth D]
2,521Homo sapiensMutation(s): 0 
Gene Names: PIEZO1FAM38AKIAA0233
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q92508 (Homo sapiens)
Explore Q92508 
Go to UniProtKB:  Q92508
PHAROS:  Q92508
GTEx:  ENSG00000103335 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92508
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
MyoD family inhibitor domain-containing proteinD [auth C],
E,
F
246Homo sapiensMutation(s): 0 
Gene Names: MDFIC
UniProt & NIH Common Fund Data Resources
Find proteins for Q9P1T7 (Homo sapiens)
Explore Q9P1T7 
Go to UniProtKB:  Q9P1T7
PHAROS:  Q9P1T7
GTEx:  ENSG00000135272 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9P1T7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
L9Q (Subject of Investigation/LOI)
Query on L9Q

Download Ideal Coordinates CCD File 
I [auth A],
J [auth B],
M [auth D]
(1S)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(octadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate
C41 H80 N O8 P
JQKOHRZNEOQNJE-VYCVAHKRSA-N
D12 (Subject of Investigation/LOI)
Query on D12

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
K [auth B]
L [auth B]
N [auth D]
G [auth A],
H [auth A],
K [auth B],
L [auth B],
N [auth D],
O [auth D],
P [auth C],
Q [auth C],
R [auth C],
S [auth E],
T [auth E],
U [auth E],
V [auth F],
W [auth F],
X [auth F]
DODECANE
C12 H26
SNRUBQQJIBEYMU-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Released Date: 2025-01-15 
  • Deposition Author(s): Zhang, M.F.

Funding OrganizationLocationGrant Number
Other governmentChina--

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-15
    Type: Initial release
  • Version 1.1: 2025-08-27
    Changes: Data collection, Database references