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- PDB-25ex: Cryo-EM structure of the Arabidopsis thaliana potassium transport... -

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Basic information

Entry
Database: PDB / ID: 25ex
TitleCryo-EM structure of the Arabidopsis thaliana potassium transporter 5 in apo state
ComponentsGreen fluorescent protein,Potassium transporter 5
KeywordsMEMBRANE PROTEIN / potassium transporter
Function / homology
Function and homology information


potassium:sodium symporter activity / potassium ion transmembrane transporter activity / potassium ion import across plasma membrane / potassium ion transport / bioluminescence / generation of precursor metabolites and energy / membrane / nucleus / plasma membrane
Similarity search - Function
Potassium transporter / : / : / K+ potassium transporter integral membrane domain / K+ potassium transporter C-terminal domain / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / : / Green fluorescent protein / Potassium transporter 5
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
Arabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.66 Å
AuthorsWang, C. / Wang, X.H. / Qu, Y.N. / Shen, H.Z.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China) China
CitationJournal: Mol Plant / Year: 2026
Title: Structural insights into the transport and gating mechanisms of the plant high-affinity K+ transporter AtHAK5
Authors: Wang, C. / Wang, X. / Qu, Y. / Shen, H.
History
DepositionMar 31, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 2, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 2, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Green fluorescent protein,Potassium transporter 5
B: Green fluorescent protein,Potassium transporter 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)259,2636
Polymers258,3302
Non-polymers9334
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Green fluorescent protein,Potassium transporter 5 / AtHAK1 / AtHAK5 / AtPOT5


Mass: 129165.008 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish), (gene. exp.) Arabidopsis thaliana (thale cress)
Gene: GFP, POT5, HAK5, At4g13420, T9E8.160 / Production host: Homo sapiens (human) / References: UniProt: P42212, UniProt: Q9M7K4
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: Potassium transporter 5 homodimer / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7
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: TFS KRIOS
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: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.17.1_3660model refinement
13PHENIX3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.66 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 905665 / Symmetry type: POINT
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00410868
ELECTRON MICROSCOPYf_angle_d0.67214766
ELECTRON MICROSCOPYf_dihedral_angle_d16.9511480
ELECTRON MICROSCOPYf_chiral_restr0.0451730
ELECTRON MICROSCOPYf_plane_restr0.0051790

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