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- EMDB-80193: Cryo-EM structure of the Arabidopsis thaliana potassium transport... -

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Basic information

Entry
Database: EMDB / ID: EMD-80193
TitleCryo-EM structure of the Arabidopsis thaliana potassium transporter mutant - K759A
Map data
Sample
  • Complex: Potassium transporter 5 homodimer
    • Protein or peptide: Potassium transporter 5
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: POTASSIUM ION
  • Ligand: water
Keywordspotassium transporter / MEMBRANE PROTEIN
Function / homology
Function and homology information


potassium:sodium symporter activity / potassium ion transmembrane transporter activity / potassium ion import across plasma membrane / potassium ion transport / membrane / nucleus / plasma membrane
Similarity search - Function
Potassium transporter / : / : / K+ potassium transporter integral membrane domain / K+ potassium transporter C-terminal domain
Similarity search - Domain/homology
Potassium transporter 5
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.26 Å
AuthorsWang C / Wang XH / Qu YN / Shen HZ
Funding support China, 1 items
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
DepositionApr 9, 2026-
Header (metadata) releaseSep 2, 2026-
Map releaseSep 2, 2026-
UpdateSep 2, 2026-
Current statusSep 2, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_80193.png

Downloads & links

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Map

FileDownload / File: emd_80193.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 256 pix.
= 278.272 Å		1.09 Å/pix.
x 256 pix.
= 278.272 Å		1.09 Å/pix.
x 256 pix.
= 278.272 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.087 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.9
Minimum - Maximum-4.66333 - 7.178358
Average (Standard dev.)0.0050695054 (±0.11524427)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 278.272 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_80193_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_80193_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Potassium transporter 5 homodimer

EntireName: Potassium transporter 5 homodimer
Components
  • Complex: Potassium transporter 5 homodimer
    • Protein or peptide: Potassium transporter 5
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: POTASSIUM ION
  • Ligand: water

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Supramolecule #1: Potassium transporter 5 homodimer

SupramoleculeName: Potassium transporter 5 homodimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: Potassium transporter 5

MacromoleculeName: Potassium transporter 5 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 89.385281 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYKDDDDKG CGRMDGEEHQ IDGDEVNNHE NKLNEKKKSW GKLYRPDSFI IEAGQTPTNT GRRSLMSWRT TMSLAFQSLG VVYGDIGTS PLYVYASTFT DGINDKDDVV GVLSLIIYTI TLVALLKYVF IVLQANDNGE GGTFALYSLI CRYAKMGLIP N QEPEDVEL ...String:
MDYKDDDDKG CGRMDGEEHQ IDGDEVNNHE NKLNEKKKSW GKLYRPDSFI IEAGQTPTNT GRRSLMSWRT TMSLAFQSLG VVYGDIGTS PLYVYASTFT DGINDKDDVV GVLSLIIYTI TLVALLKYVF IVLQANDNGE GGTFALYSLI CRYAKMGLIP N QEPEDVEL SNYTLELPTT QLRRAHMIKE KLENSKFAKI ILFLVTIMGT SMVIGDGILT PSISVLSAVS GIKSLGQNTV VG VSVAILI VLFAFQRFGT DKVGFSFAPI ILVWFTFLIG IGLFNLFKHD ITVLKALNPL YIIYYFRRTG RQGWISLGGV FLC ITGTEA MFADLGHFSV RAVQISFSCV AYPALVTIYC GQAAYLTKHT YNVSNTFYDS IPDPLYWPTF VVAVAASIIA SQAM ISGAF SVISQSLRMG CFPRVKVVHT SAKYEGQVYI PEINYLLMLA CIAVTLAFRT TEKIGHAYGI AVVTVMVITT LMVTL IMLV IWKTNIVWIA IFLVVFGSIE MLYLSSVMYK FTSGGYLPLT ITVVLMAMMA IWQYVHVLKY RYELREKISR ENAIQM ATS PDVNRVPGIG LFYTELVNGI TPLFSHYISN LSSVHSVFVL ISIKTLPVNR VTSSERFFFR YVGPKDSGMF RCVVRYG YK EDIEEPDEFE RHFVYYLKEF IHHEHFMSGG GGEVDETDKE EEPNAETTVV PSSNYVPSSG RIGSAHSSSS DKIRSGRV V QVQSVEDQTE LVEKAREKGM VYLMGETEIT AEKESSLFKK FIVNHAYNFL AKNCREGDKA LAIPRSKLLK VGMTYEL

UniProtKB: Potassium transporter 5

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Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 2 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #3: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: K
Molecular weightTheoretical: 39.098 Da

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 12 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 4.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 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: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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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: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: PHENIX / Number images used: 236347
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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