7XUF | pdb_00007xuf

Cryo-EM structure of the AKT1-AtKC1 complex from Arabidopsis thaliana


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Structural basis for the activity regulation of a potassium channel AKT1 from Arabidopsis.

Lu, Y.Yu, M.Jia, Y.Yang, F.Zhang, Y.Xu, X.Li, X.Yang, F.Lei, J.Wang, Y.Yang, G.

(2022) Nat Commun 13: 5682-5682

  • DOI: https://doi.org/10.1038/s41467-022-33420-8
  • Primary Citation Related Structures: 
    7FCV, 7WSW, 7XUF

  • PubMed Abstract: 

    The voltage-gated potassium channel AKT1 is responsible for primary K + uptake in Arabidopsis roots. AKT1 is functionally activated through phosphorylation and negatively regulated by a potassium channel α-subunit AtKC1. However, the molecular basis for the modulation mechanism remains unclear. Here we report the structures of AKT1, phosphorylated-AKT1, a constitutively-active variant, and AKT1-AtKC1 complex. AKT1 is assembled in 2-fold symmetry at the cytoplasmic domain. Such organization appears to sterically hinder the reorientation of C-linkers during ion permeation. Phosphorylated-AKT1 adopts an alternate 4-fold symmetric conformation at cytoplasmic domain, which indicates conformational changes associated with symmetry switch during channel activation. To corroborate this finding, we perform structure-guided mutagenesis to disrupt the dimeric interface and identify a constitutively-active variant Asp379Ala mediates K + permeation independently of phosphorylation. This variant predominantly adopts a 4-fold symmetric conformation. Furthermore, the AKT1-AtKC1 complex assembles in 2-fold symmetry. Together, our work reveals structural insight into the regulatory mechanism for AKT1.


  • Organizational Affiliation
    • State Key Laboratory for Agrobiotechnology, Frontiers Science Center for Molecular Design Breeding, College of Biological Sciences, China Agricultural University, Beijing, China.

Macromolecule Content 

  • Total Structure Weight: 345.71 kDa 
  • Atom Count: 15,041 
  • Modeled Residue Count: 1,864 
  • Deposited Residue Count: 3,038 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Potassium channel KAT3
A, C
662Arabidopsis thalianaMutation(s): 0 
Gene Names: KAT3AKT4KC1At4g32650F4D11.150
Membrane Entity: Yes 
UniProt
Find proteins for P92960 (Arabidopsis thaliana)
Explore P92960 
Go to UniProtKB:  P92960
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP92960
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Potassium channel AKT1
B, D
857Arabidopsis thalianaMutation(s): 0 
Gene Names: AKT1
Membrane Entity: Yes 
UniProt
Find proteins for Q38998 (Arabidopsis thaliana)
Explore Q38998 
Go to UniProtKB:  Q38998
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ38998
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-09
    Type: Initial release
  • Version 1.1: 2024-07-03
    Changes: Data collection
  • Version 1.2: 2025-06-18
    Changes: Data collection, Structure summary