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- EMDB-66431: Cryo-EM structure of AKT5 - WT -

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Basic information

Entry
Database: EMDB / ID: EMD-66431
TitleCryo-EM structure of AKT5 - WT
Map data
Sample
  • Complex: Homotetramer of AKT5
    • Protein or peptide: Probable potassium channel AKT5
KeywordsTetramer / TRANSPORT PROTEIN
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)
Methodsingle 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, 1 items
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, 2025-
Header (metadata) releaseJul 15, 2026-
Map releaseJul 15, 2026-
UpdateSep 9, 2026-
Current statusSep 9, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_66431.png

Downloads & links

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Map

FileDownload / File: emd_66431.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.81 Å/pix.
x 448 pix.
= 361.088 Å		0.81 Å/pix.
x 448 pix.
= 361.088 Å		0.81 Å/pix.
x 448 pix.
= 361.088 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.806 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.13
Minimum - Maximum-0.6140569 - 0.82102036
Average (Standard dev.)0.000541814 (±0.013614776)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 361.088 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_66431_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_66431_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Homotetramer of AKT5

EntireName: Homotetramer of AKT5
Components
  • Complex: Homotetramer of AKT5
    • Protein or peptide: Probable potassium channel AKT5

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Supramolecule #1: Homotetramer of AKT5

SupramoleculeName: Homotetramer of AKT5 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: Probable potassium channel AKT5

MacromoleculeName: Probable potassium channel AKT5 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 100.450242 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MDYKDDDDKG IEKRKKMVWF WPEKHEGGVI KEAEDVAAEH ISREGTMSHY SFSKGLLPPL GVGATARSSR HIKLRCFIVS PFDPRYRAW DWFLVILVLY TAWASPFEFG FLQTPRAPLS ILDNVVNGFF AVDIVLTFFV AFLDKATYLL VDDPKRIAWR Y TSTWLIFD ...String:
MDYKDDDDKG IEKRKKMVWF WPEKHEGGVI KEAEDVAAEH ISREGTMSHY SFSKGLLPPL GVGATARSSR HIKLRCFIVS PFDPRYRAW DWFLVILVLY TAWASPFEFG FLQTPRAPLS ILDNVVNGFF AVDIVLTFFV AFLDKATYLL VDDPKRIAWR Y TSTWLIFD VVSTVPYELF GSLLHNTIQG YGIFSMLRLW RLHRVSKCFA RLEKDRKYNY FWIRCTKLLL VSLFVVHCGA CF CYSIAAH YPDPSMTFMA LAEANWKQKS LLIRYVTAMY WSITTFSTTG YGDIHGNNAE ERAFILFYMI FNLGLLAYII GNM TNLVVH VTSRTRNFRD TIQAASAFAQ RNNLPLGLQE QMVAHLSLRY RTDSEGLQQQ EIIDSLPKAI RSSISHYLFY EVVD KTYLF HGISNDLLFQ LVSEMKAEYF PPKEDVILRN EAPSDFYIMV TGAVDIIARV NGVDQVVGEA QTGHVFGEVG VLCYR PQLF TVRTKRLSQL LRLNRTAFLN LVQANVGDGA IIMNNLLQHL KDSTDPVMKG ILAETELMLA QGKMDLPLSL CFAAAR GDD LLLHQLLKRG SNPNETDKNG RTALHIAASK GSQYCVVLLL EHGADPNIRD SEGSVPLWEA IIGRHEENAK LLSENGA TL SFDTVGYFSC LAVGQNNLNA LKDIVKYGGD ISLSDVNGTT ALHRAVSEGN LEIVQFLLEK GADMDKPDVY GWTARALA E HQGHEDIKAL FYNQRPVERK TILVSGTPEI KPLMKHSSEP VMTHHHSREA MPPLARAVSQ RRKLSNFKNS LFGIMSAAK TGDEGGASTR TGISEGVGGV YPARVTISGE ASSSGKVVKL PDSLEELIEI GEKKLGFVAT KILSREGAEI DDIRIIRDGD FLLLLKVSH HHHHH

UniProtKB: Probable potassium channel AKT5

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.62 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 54571
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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