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- EMDB-36195: Conformation 1 of the plant potassium channel SKOR -

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Basic information

Entry
Database: EMDB / ID: EMD-36195
TitleConformation 1 of the plant potassium channel SKOR
Map data
Sample
  • Complex: Tetrameric SKOR complex
    • Protein or peptide: Potassium channel SKOR
Keywordsvoltage-gated potassium channel / outward-rectifier / symmetry reduction / ploy-ankyrin domain / PLANT PROTEIN
Function / homology
Function and homology information


potassium ion homeostasis / outward rectifier potassium channel activity / monoatomic ion channel complex / potassium ion transport
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 SKOR
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsLiu S / Li S / Sun D / Tian C
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21825703 China
National Natural Science Foundation of China (NSFC)32000854 China
CitationJournal: Cell Discov / Year: 2023
Title: Cryo-EM structure reveals a symmetry reduction of the plant outward-rectifier potassium channel SKOR.
Authors: Siyu Li / Yuanxia Wang / Chenyang Wang / Yong Zhang / Demeng Sun / Peng Zhou / Changlin Tian / Sanling Liu /
History
DepositionMay 16, 2023-
Header (metadata) releaseAug 30, 2023-
Map releaseAug 30, 2023-
UpdateAug 30, 2023-
Current statusAug 30, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36195.png

Downloads & links

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Map

FileDownload / File: emd_36195.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 320 pix.
= 323.2 Å		1.01 Å/pix.
x 320 pix.
= 323.2 Å		1.01 Å/pix.
x 320 pix.
= 323.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.01 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.22
Minimum - Maximum-0.63913965 - 1.2775164
Average (Standard dev.)0.0026395852 (±0.07594537)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 323.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_36195_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_36195_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 : Tetrameric SKOR complex

EntireName: Tetrameric SKOR complex
Components
  • Complex: Tetrameric SKOR complex
    • Protein or peptide: Potassium channel SKOR

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Supramolecule #1: Tetrameric SKOR complex

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

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Macromolecule #1: Potassium channel SKOR

MacromoleculeName: Potassium channel SKOR / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 94.011062 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGGSSGGGVS YRSGGESDVE LEDYEVDDFR DGIVESRGNR FNPLTNFLGL DFAGGSGGKF TVINGIRDIS RGSIVHPDNR WYKAWTMFI LIWALYSSFF TPLEFGFFRG LPENLFILDI AGQIAFLVDI VLTFFVAYRD SRTYRMIYKR SSIALRYLKS T FIIDLLAC ...String:
MGGSSGGGVS YRSGGESDVE LEDYEVDDFR DGIVESRGNR FNPLTNFLGL DFAGGSGGKF TVINGIRDIS RGSIVHPDNR WYKAWTMFI LIWALYSSFF TPLEFGFFRG LPENLFILDI AGQIAFLVDI VLTFFVAYRD SRTYRMIYKR SSIALRYLKS T FIIDLLAC MPWDIIYKAA GEKEEVRYLL LIRLYRVHRV ILFFHKMEKD IRINYLFTRI VKLIFVELYC THTAACIFYY LA TTLPASQ EGYTWIGSLK LGDYSYSKFR EIDLWTRYTT SMYFAVVTMA TVGYGDIHAV NMREMIFAMV YISFDMILGA YLI GNMTAL IVKGSKTERF RDKMADIMRY MNRNKLGRNI RGQITGHLRL QYESSYTEAA VLQDIPVSIR AKIAQTLYLP YIEK VPLFR GCSSEFINQI VIRLHEEFFL PGEVIMEQGS VVDQLYFVCH GVLEEIGITK DGSEEIVAVL QPDHSFGEIS ILCNI PQPY TVRVAELCRI LRLDKQSFMN ILEIFFHDGR RILNNLLEGK ESNVRIKQLE SDITFHISKQ EAELALKLNS AAFYGD LYQ LKSLIRAGGD PNKTDYDGRS PLHLAASRGY EDITLYLIQE SVDVNIKDKL GSTPLLEAIK NGNDRVAALL VKEGATL NI ENAGTFLCTV VAKGDSDFLK RLLSNGIDPN SKDYDHRTPL HVAASEGFYV LAIQLVEASA NVLAKDRWGN TPLDEALG C GNKMLIKLLE DAKNSQISSF PSGSKEPKDK VYKKKCTVYF SHPGDSKEKR RRGIVLWVPR SIEELIRTAK EQLNVPEAS CVLSEDEAKI IDVDLISDGQ KLYLAVET

UniProtKB: Potassium channel SKOR

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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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 56.0 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: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 129992
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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