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- EMDB-80068: Cryo-EM structure of the Arabidopsis thaliana potassium transport... -

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Basic information

Entry
Database: EMDB / ID: EMD-80068
TitleCryo-EM structure of the Arabidopsis thaliana potassium transporter 5 in apo state
Map data
Sample
  • Complex: Potassium transporter 5 homodimer
    • Protein or peptide: Green fluorescent protein,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 / 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
Green fluorescent protein / Potassium transporter 5
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.66 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
DepositionMar 31, 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_80068.png

Downloads & links

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Map

FileDownload / File: emd_80068.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 240 pix.
= 258.552 Å		1.08 Å/pix.
x 240 pix.
= 258.552 Å		1.08 Å/pix.
x 240 pix.
= 258.552 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0773 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.31
Minimum - Maximum-6.627413 - 9.750397
Average (Standard dev.)0.0036381355 (±0.21568112)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 258.552 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_80068_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_80068_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 : Potassium transporter 5 homodimer

EntireName: Potassium transporter 5 homodimer
Components
  • Complex: Potassium transporter 5 homodimer
    • Protein or peptide: Green fluorescent protein,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: Green fluorescent protein,Potassium transporter 5

MacromoleculeName: Green fluorescent protein,Potassium transporter 5 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 129.165008 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGGEGLRASP RRRPLLPLQP RGCPRGDGCL RGGRGRAGFG FWRVTGGSRA SANHVHAFFF FLQLLGNVLV IVLSHHFGKE FATMAHHHH HHHHAADYKD HDIDYKDDDD KSAMVSKGEE LFTGVVPILV ELDGDVNGHK FSVSGEGEGD ATYGKLTLKF I CTTGKLPV ...String:
MGGEGLRASP RRRPLLPLQP RGCPRGDGCL RGGRGRAGFG FWRVTGGSRA SANHVHAFFF FLQLLGNVLV IVLSHHFGKE FATMAHHHH HHHHAADYKD HDIDYKDDDD KSAMVSKGEE LFTGVVPILV ELDGDVNGHK FSVSGEGEGD ATYGKLTLKF I CTTGKLPV PWPTLVTTLT YGVQCFSRYP DHMKQHDFFK SAMPEGYVQE RTIFFKDDGN YTTRAEVKFE GDTLVNRIEL KG IDFKEDG NILGHKLEYN YNSHNVYIMA DKQKNGIKVN FKIRHNIEDG SVQLADHYQQ NTPIGDGPVL LPDNHYLSTQ SKL SKDPNE KRDHMVLLEF VTAAGITLGM DELYKSGLRS GLEVLFQGPG GRMDGEEHQI DGDEVNNHEN KLNEKKKSWG KLYR PDSFI IEAGQTPTNT GRRSLMSWRT TMSLAFQSLG VVYGDIGTSP LYVYASTFTD GINDKDDVVG VLSLIIYTIT LVALL KYVF IVLQANDNGE GGTFALYSLI CRYAKMGLIP NQEPEDVELS NYTLELPTTQ LRRAHMIKEK LENSKFAKII LFLVTI MGT SMVIGDGILT PSISVLSAVS GIKSLGQNTV VGVSVAILIV LFAFQRFGTD KVGFSFAPII LVWFTFLIGI GLFNLFK HD ITVLKALNPL YIIYYFRRTG RQGWISLGGV FLCITGTEAM FADLGHFSVR AVQISFSCVA YPALVTIYCG QAAYLTKH T YNVSNTFYDS IPDPLYWPTF VVAVAASIIA SQAMISGAFS VISQSLRMGC FPRVKVVHTS AKYEGQVYIP EINYLLMLA CIAVTLAFRT TEKIGHAYGI AVVTVMVITT LMVTLIMLVI WKTNIVWIAI FLVVFGSIEM LYLSSVMYKF TSGGYLPLTI TVVLMAMMA IWQYVHVLKY RYELREKISR ENAIQMATSP DVNRVPGIGL FYTELVNGIT PLFSHYISNL SSVHSVFVLI S IKTLPVNR VTSSERFFFR YVGPKDSGMF RCVVRYGYKE DIEEPDEFER HFVYYLKEFI HHEHFMSGGG GEVDETDKEE EP NAETTVV PSSNYVPSSG RIGSAHSSSS DKIRSGRVVQ VQSVEDQTEL VEKAREKGMV YLMGETEITA EKESSLFKKF IVN HAYNFL KKNCREGDKA LAIPRSKLLK VGMTYEL

UniProtKB: Green fluorescent protein, 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: 7
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: 2.66 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: PHENIX / Number images used: 905665
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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