8IXN | pdb_00008ixn

Curved structure of mPIEZO1-S2472E


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.07 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

An intermediate open structure reveals the gating transition of the mechanically activated PIEZO1 channel.

Liu, S.Yang, X.Chen, X.Zhang, X.Jiang, J.Yuan, J.Liu, W.Wang, L.Zhou, H.Wu, K.Tian, B.Li, X.Xiao, B.

(2025) Neuron 113: 590

  • DOI: https://doi.org/10.1016/j.neuron.2024.11.020
  • Primary Citation of Related Structures:  
    8IXN, 8IXO

  • PubMed Abstract: 

    PIEZO1 is a mechanically activated cation channel that undergoes force-induced activation and inactivation. However, its distinct structural states remain undefined. Here, we employed an open-prone PIEZO1-S2472E mutant to capture an intermediate open structure. Compared with the curved and flattened structures of PIEZO1, the S2472E-Intermediate structure displays partially flattened blades, a downward and rotational motion of the top cap, and a spring-like compression of the linker connecting the cap to the pore-lining inner helix. These conformational changes open the cap gate and the hydrophobic transmembrane gate, whereas the intracellular lateral plug gate remains closed. The flattened structure of PIEZO1 with an up-state cap and closed cap gate might represent an inactivated state. Molecular dynamics (MD) simulations of ion conduction support the closed, intermediate open, and inactivated structural states. Mutagenesis and electrophysiological studies identified key domains and residues critical for the mechanical activation of PIEZO1. These studies collectively define the distinct structural states and gating transitions of PIEZO1.


  • Organizational Affiliation
    • State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center of Biological Structure, Tsinghua University, Beijing 100084, China; MOE Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Piezo-type mechanosensitive ion channel component 1A [auth C],
B [auth A],
C [auth D]
2,547Mus musculusMutation(s): 1 
Gene Names: Piezo1Fam38a
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for E2JF22 (Mus musculus)
Explore E2JF22 
Go to UniProtKB:  E2JF22
IMPC:  MGI:3603204
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE2JF22
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
P5S (Subject of Investigation/LOI)
Query on P5S

Download Ideal Coordinates CCD File 
G [auth C],
K [auth A],
O [auth D]
O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
C42 H82 N O10 P
TZCPCKNHXULUIY-RGULYWFUSA-N
PLX (Subject of Investigation/LOI)
Query on PLX

Download Ideal Coordinates CCD File 
D [auth C]
E [auth C]
H [auth A]
I [auth A]
L [auth D]
D [auth C],
E [auth C],
H [auth A],
I [auth A],
L [auth D],
M [auth D]
(9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,7,10-TRIOXA-2LAMBDA~5~-AZA-6LAMBDA~5~-PHOSPHAOCTACOSANE-6,6,11-TRIOL
C42 H89 N O8 P
YVNJQRQLQPWVSQ-IWSHAHEXSA-O
PEE (Subject of Investigation/LOI)
Query on PEE

Download Ideal Coordinates CCD File 
F [auth C],
J [auth A],
N [auth D]
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
C41 H78 N O8 P
MWRBNPKJOOWZPW-NYVOMTAGSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.07 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other government2016YFA0500402
National Natural Science Foundation of China (NSFC)China31825014
National Natural Science Foundation of China (NSFC)China32130049
National Natural Science Foundation of China (NSFC)China32021002
National Natural Science Foundation of China (NSFC)China31630090

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-01
    Type: Initial release
  • Version 1.1: 2025-03-05
    Changes: Data collection, Database references
  • Version 1.2: 2025-06-25
    Changes: Data collection