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- EMDB-36199: Intracellular domain of the plant potassium channel SKOR mutant -... -

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Basic information

Entry
Database: EMDB / ID: EMD-36199
TitleIntracellular domain of the plant potassium channel SKOR mutant - L271P/D312N
Map data
Sample
  • Complex: Tetrameric SKOR complex - L271P/D312N mutant
    • Protein or peptide: Stellar K+ Outward Rectifier (SKOR) channel
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: 3.6 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) releaseSep 20, 2023-
Map releaseSep 20, 2023-
UpdateSep 20, 2023-
Current statusSep 20, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36199.png

Downloads & links

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Map

FileDownload / File: emd_36199.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: 0.36
Minimum - Maximum-1.9600514 - 3.263461
Average (Standard dev.)-0.0027464891 (±0.06126873)
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: #1

Fileemd_36199_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_36199_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 - L271P/D312N mutant

EntireName: Tetrameric SKOR complex - L271P/D312N mutant
Components
  • Complex: Tetrameric SKOR complex - L271P/D312N mutant
    • Protein or peptide: Stellar K+ Outward Rectifier (SKOR) channel

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Supramolecule #1: Tetrameric SKOR complex - L271P/D312N mutant

SupramoleculeName: Tetrameric SKOR complex - L271P/D312N mutant / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: Stellar K+ Outward Rectifier (SKOR) channel

MacromoleculeName: Stellar K+ Outward Rectifier (SKOR) channel / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
SequenceString: MGGSSGGGVS YRSGGESDVE LEDYEVDDFR DGIVESRGNR FNPLTNFLGL DFAGGSGGKF TVINGIRDI SRGSIVHPDN RWYKAWTMFI LIWALYSSFF TPLEFGFFRG LPENLFILDI A GQIAFLVD IVLTFFVAYR DSRTYRMIYK RSSIALRYLK STFIIDLLAC ...String:
MGGSSGGGVS YRSGGESDVE LEDYEVDDFR DGIVESRGNR FNPLTNFLGL DFAGGSGGKF TVINGIRDI SRGSIVHPDN RWYKAWTMFI LIWALYSSFF TPLEFGFFRG LPENLFILDI A GQIAFLVD IVLTFFVAYR DSRTYRMIYK RSSIALRYLK STFIIDLLAC MPWDIIYKAA GE KEEVRYL LLIRLYRVHR VILFFHKMEK DIRINYLFTR IVKLIFVELY CTHTAACIFY YLA TTLPAS QEGYTWIGSL KLGDYSYSKF REIDPWTRYT TSMYFAVVTM ATVGYGDIHA VNMR EMIFA MVYISFNMIL GAYLIGNMTA LIVKGSKTER FRDKMADIMR YMNRNKLGRN IRGQI TGHL RLQYESSYTE AAVLQDIPVS IRAKIAQTLY LPYIEKVPLF RGCSSEFINQ IVIRLH EEF FLPGEVIMEQ GSVVDQLYFV CHGVLEEIGI TKDGSEEIVA VLQPDHSFGE ISILCNI PQ PYTVRVAELC RILRLDKQSF MNILEIFFHD GRRILNNLLE GKESNVRIKQ LESDITFH I SKQEAELALK LNSAAFYGDL YQLKSLIRAG GDPNKTDYDG RSPLHLAASR GYEDITLYL IQESVDVNIK DKLGSTPLLE AIKNGNDRVA ALLVKEGATL NIENAGTFLC TVVAKGDSDF LKRLLSNGI DPNSKDYDHR TPLHVAASEG FYVLAIQLVE ASANVLAKDR WGNTPLDEAL G CGNKMLIK LLEDAKNSQI SSFPSGSKEP KDKVYKKKCT VYFSHPGDSK EKRRRGIVLW VP RSIEELI RTAKEQLNVP EASCVLSEDE AKIIDVDLIS DGQKLYLAVE T

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: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 97194
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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