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- PDB-9x0b: Cryo-EM structure of AKT5 - WT -

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Basic information

Entry
Database: PDB / ID: 9x0b
TitleCryo-EM structure of AKT5 - WT
ComponentsProbable potassium channel AKT5
KeywordsTRANSPORT PROTEIN / Tetramer
Function / homology
Function and homology information


monoatomic ion channel complex / voltage-gated potassium channel activity
Similarity search - Function
Potassium channel KAT/AKT / KHA domain / KHA, dimerisation domain of potassium ion channel / KHA domain profile. / Potassium channel, voltage-dependent, EAG/ELK/ERG / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily ...Potassium channel KAT/AKT / KHA domain / KHA, dimerisation domain of potassium ion channel / KHA domain profile. / Potassium channel, voltage-dependent, EAG/ELK/ERG / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / RmlC-like jelly roll fold / Ankyrin repeat profile. / Ankyrin repeats (3 copies) / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Probable potassium channel AKT5
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.62 Å
AuthorsMuraoka, Y. / Tanaka, Y. / Yokoyama, T. / Furuta, T. / Yamanashi, T. / Tsujii, M. / Tsubota, R. / Uozumi, N.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan) Japan
CitationJournal: Sci Adv / Year: 2026
Title: AKT5 is a bona fide potassium channel and controls petiole growth in .
Authors: Yuki Muraoka / Shunsuke Kobayashi / Lisa Oskam / Michihiro Tateyama / Ayumu Masago / Yoshikazu Tanaka / Takeshi Yokoyama / Tadaomi Furuta / Hinano Takase / Ellen Tanudjaja / Shota Terashima ...Authors: Yuki Muraoka / Shunsuke Kobayashi / Lisa Oskam / Michihiro Tateyama / Ayumu Masago / Yoshikazu Tanaka / Takeshi Yokoyama / Tadaomi Furuta / Hinano Takase / Ellen Tanudjaja / Shota Terashima / Haruto Shimizukawa / Taro Yamanashi / Shunya Saito / Hiroki Ijima / Miyuki Tanaka / Atsushi Miyamoto / Megumi Kato / Kanane Sato / Masaru Tsujii / Taishi Umezawa / Francisco J Quintero / Francisco Rubio / Jörg Kudla / Masaaki Ito / Yoshihiro Kubo / Yasuhiro Ishimaru / Ronald Pierik / Nobuyuki Uozumi /
Abstract: Potassium ion (K) is essential for plant growth and development. Despite decades of study, the -type K channel AKT5 has remained functionally unassigned. Here, we report that AKT5 functions as a bona ...Potassium ion (K) is essential for plant growth and development. Despite decades of study, the -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.
History
DepositionSep 30, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 15, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable potassium channel AKT5
B: Probable potassium channel AKT5
C: Probable potassium channel AKT5
D: Probable potassium channel AKT5


Theoretical massNumber of molelcules
Total (without water)401,8014
Polymers401,8014
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Probable potassium channel AKT5


Mass: 100450.242 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AKT5, At4g32500, F8B4.200 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9SCX5
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Homotetramer of AKT5 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.2_5419model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.62 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 54571 / Symmetry type: POINT
RefinementHighest resolution: 3.62 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

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