9C49

Cryo-EM structure of Danio rerio voltage-sensing phosphatase (VSP) phosphatase domain


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.97 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

Coupling sensor to enzyme in the voltage sensing phosphatase.

Yu, Y.Zhang, L.Li, B.Fu, Z.Brohawn, S.G.Isacoff, E.Y.

(2024) Nat Commun 15: 6409-6409

  • DOI: https://doi.org/10.1038/s41467-024-50319-8
  • Primary Citation of Related Structures:  
    9C49

  • PubMed Abstract: 

    Voltage-sensing phosphatases (VSPs) dephosphorylate phosphoinositide (PIP) signaling lipids in response to membrane depolarization. VSPs possess an S4-containing voltage sensor domain (VSD), resembling that of voltage-gated cation channels, and a lipid phosphatase domain (PD). The mechanism by which voltage turns on enzyme activity is unclear. Structural analysis and modeling suggest several sites of VSD-PD interaction that could couple voltage sensing to catalysis. Voltage clamp fluorometry reveals voltage-driven rearrangements in three sites implicated earlier in enzyme activation-the VSD-PD linker, gating loop and R loop-as well as the N-terminal domain, which has not yet been explored. N-terminus mutations perturb both rearrangements in the other segments and enzyme activity. Our results provide a model for a dynamic assembly by which S4 controls the catalytic site.


  • Organizational Affiliation

    Department of Molecular and Cell Biology, University of California, Berkeley, California, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase TPTE2
A, B
520Danio rerioMutation(s): 1 
Gene Names: tptetpipvspwu:fd20e11wu:fi24b06
EC: 3.1.3.48
UniProt
Find proteins for Q4V9E4 (Danio rerio)
Explore Q4V9E4 
Go to UniProtKB:  Q4V9E4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4V9E4
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.97 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM145869

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-10
    Type: Initial release
  • Version 1.1: 2024-08-14
    Changes: Data collection, Database references