9X0C | pdb_00009x0c

Cryo-EM structure of AKT5 - D403A

• PDB DOI: https://doi.org/10.2210/pdb9X0C/pdb
• EM Map EMD-66432: EMDB EMDataResource

• Classification: TRANSPORT PROTEIN
• Organism(s): Arabidopsis thaliana
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2025-09-30 Released: 2026-07-15 
• Deposition Author(s): Muraoka, Y., Tanaka, Y., Yokoyama, T., Furuta, T., Yamanashi, T., Tsujii, M., Tsubota, R., Uozumi, N.
• Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology (Japan)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

AKT5 is a bona fide potassium channel and controls petiole growth in Arabidopsis.

Muraoka, Y., Kobayashi, S., Oskam, L., Tateyama, M., Masago, A., Tanaka, Y., Yokoyama, T., Furuta, T., Takase, H., Tanudjaja, E., Terashima, S., Shimizukawa, H., Yamanashi, T., Saito, S., Ijima, H., Tanaka, M., Miyamoto, A., Kato, M., Sato, K., Tsujii, M., Umezawa, T., Quintero, F.J., Rubio, F., Kudla, J., Ito, M., Kubo, Y., Ishimaru, Y., Pierik, R., Uozumi, N.

(2026) Sci Adv 12: eaeh7630-eaeh7630

• PubMed: 42685185 
• DOI: https://doi.org/10.1126/sciadv.aeh7630
• Primary Citation Related Structures: 
  9X0B, 9X0C


• PubMed Abstract: 
  

  Potassium ion (K ⁺ ) is essential for plant growth and development. Despite decades of study, the Shaker -type K ⁺ channel AKT5 has remained functionally unassigned. Here, we report that AKT5 functions as a bona fide voltage-dependent K ⁺ channel and serves as an essential regulator of petiole elongation. Structural analyses of AKT5 in a closed state and the AKT5-D403 variant in a pre-open state provide direct structural evidence for functional K ⁺ channel activity. AKT5 assembled into a canonical tetramer with two-fold symmetry and, upon phosphorylation, operated as an inward-rectifying K ⁺ channel activated at strongly hyperpolarized membrane potentials. AKT5 was predominantly expressed in young petioles, and loss of AKT5 function largely suppressed petiole elongation throughout the diurnal cycle, resulting in compact rosettes and reduced biomass under crowded growth conditions. These findings show that AKT5 is involved in a regulator of plant competitive growth and high-density performance.

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Organizational Affiliation: 
• Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University; Sendai, 980-8579, Japan.
Laboratory of Molecular Biology, Wageningen University and Research; Wageningen, 6708 TB, The Netherlands.
Division of Biophysics and Neurobiology, Department of Molecular and Cellular Physiology, National Institute for Physiological Sciences; Okazaki, 444-8585, Japan.
Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University; Sendai, 980-8577, Japan.
School of Life Science and Technology, Institute of Science Tokyo; Yokohama, 226-8501, Japan.
Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology; Koganei, 184-8588, Japan.
Institute of Plant Biochemistry and Photosynthesis, Consejo Superior de Investigaciones Cientificas and University of Seville; Seville, 41092, Spain.
Departamento de Nutrición Vegetal, CEBAS-CSIC, Campus de Espinardo; Murcia, 30100, Spain.
Institut für Biologie und Biotechnologie der Pflanzen, Universität Münster; Münster, 48149, Germany.
Department of Bioresources Engineering, National Institute of Technology, Okinawa College; Nago, 905-2192, Japan.

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 401.62 kDa 
• Atom Count: 14,592 
• Modeled Residue Count: 1,796 
• Deposited Residue Count: 3,576 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable potassium channel AKT5	A [auth B], B [auth C], C [auth A], D	894	Arabidopsis thaliana	Mutation(s): 1  Gene Names: AKT5, At4g32500, F8B4.200
UniProt
Find proteins for Q9SCX5 (Arabidopsis thaliana) Explore Q9SCX5  Go to UniProtKB:  Q9SCX5

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-07-15 
Deposition Author(s): Muraoka, Y., Tanaka, Y., Yokoyama, T., Furuta, T., Yamanashi, T., Tsujii, M., Tsubota, R., Uozumi, N.

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Funding Organization	Location	Grant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	--

Revision History  

• Version 1.0: 2026-07-15
  Type: Initial release
  
• Version 1.1: 2026-09-09
  Changes: Data collection, Database references