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- PDB-7xuf: Cryo-EM structure of the AKT1-AtKC1 complex from Arabidopsis thaliana -

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Basic information

Entry
Database: PDB / ID: 7xuf
TitleCryo-EM structure of the AKT1-AtKC1 complex from Arabidopsis thaliana
Components
  • Potassium channel AKT1
  • Potassium channel KAT3
KeywordsMEMBRANE PROTEIN / Complex / Potassium channel
Function / homology
Function and homology information


root hair elongation / regulation of stomatal closure / response to water deprivation / inward rectifier potassium channel activity / response to nematode / potassium ion import across plasma membrane / monoatomic ion channel complex / voltage-gated potassium channel activity / response to salt stress / potassium ion transmembrane transport ...root hair elongation / regulation of stomatal closure / response to water deprivation / inward rectifier potassium channel activity / response to nematode / potassium ion import across plasma membrane / monoatomic ion channel complex / voltage-gated potassium channel activity / response to salt stress / potassium ion transmembrane transport / potassium ion transport / endoplasmic reticulum / identical protein binding / plasma membrane
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 repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
: / Potassium channel KAT3 / Potassium channel AKT1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsYang, G.H. / Lu, Y.M. / Jia, Y.T. / Yang, F. / Zhang, Y.M. / Xu, X. / Li, X.M. / Lei, J.L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2022
Title: Structural basis for the activity regulation of a potassium channel AKT1 from Arabidopsis.
Authors: Yaming Lu / Miao Yu / Yutian Jia / Fan Yang / Yanming Zhang / Xia Xu / Xiaomin Li / Fan Yang / Jianlin Lei / Yi Wang / Guanghui Yang /
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 ...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.
History
DepositionMay 18, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
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Revision 1.1Jul 3, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update
Revision 1.2Jun 18, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details
Item: _em_admin.last_update / _em_software.name / _pdbx_entry_details.has_protein_modification
Revision 1.1Jun 18, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Potassium channel KAT3
B: Potassium channel AKT1
C: Potassium channel KAT3
D: Potassium channel AKT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)345,7137
Polymers345,5954
Non-polymers1173
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Potassium channel KAT3 / AKT4 / AtKC1 / Potassium channel TKC


Mass: 75688.023 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: KAT3, AKT4, KC1, At4g32650, F4D11.150 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P92960
#2: Protein Potassium channel AKT1


Mass: 97109.625 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AKT1 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q38998
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
Has ligand of interestN
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: Arabidopsis thaliana AKT1-AtKC1 complex / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 1.5959 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.1_4122: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 104142 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00315410
ELECTRON MICROSCOPYf_angle_d0.54220916
ELECTRON MICROSCOPYf_dihedral_angle_d4.5332050
ELECTRON MICROSCOPYf_chiral_restr0.0412376
ELECTRON MICROSCOPYf_plane_restr0.0042618

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