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- EMDB-37847: potassium outward rectifier channel SKOR -

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Basic information

Entry
Database: EMDB / ID: EMD-37847
Titlepotassium outward rectifier channel SKOR
Map data
Sample
  • Complex: SKOR
    • Protein or peptide: Potassium channel SKOR
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
KeywordsPotassium transport / Cryo-EM / ion channel / tetramer / METAL TRANSPORT
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
AuthorsGao X / Sun T / Lu Y / Jia Y / Xu X / Zhang Y / Fu P / Yang G
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171188 China
CitationJournal: Plant Commun / Year: 2024
Title: Structural changes in the conversion of an Arabidopsis outward-rectifying K channel into an inward-rectifying channel.
Authors: Xudong Gao / Xia Xu / Tengfei Sun / Yuhan Lu / Yutian Jia / Jiaqi Zhou / Peng Fu / Yanming Zhang / Guanghui Yang /
History
DepositionOct 19, 2023-
Header (metadata) releaseApr 10, 2024-
Map releaseApr 10, 2024-
UpdateJun 26, 2024-
Current statusJun 26, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37847.png

Downloads & links

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Map

FileDownload / File: emd_37847.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 280 pix.
= 291.2 Å		1.04 Å/pix.
x 280 pix.
= 291.2 Å		1.04 Å/pix.
x 280 pix.
= 291.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.249
Minimum - Maximum-1.6671412 - 2.398788
Average (Standard dev.)0.0018502943 (±0.047463037)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 291.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_37847_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_37847_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 : SKOR

EntireName: SKOR
Components
  • Complex: SKOR
    • Protein or peptide: Potassium channel SKOR
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE

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Supramolecule #1: SKOR

SupramoleculeName: SKOR / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
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: 95.146195 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: DYKDDDDKHM GGSSGGGVSY RSGGESDVEL EDYEVDDFRD GIVESRGNRF NPLTNFLGLD FAGGSGGKFT VINGIRDISR GSIVHPDNR WYKAWTMFIL IWALYSSFFT PLEFGFFRGL PENLFILDIA GQIAFLVDIV LTFFVAYRDS RTYRMIYKRS S IALRYLKS ...String:
DYKDDDDKHM GGSSGGGVSY RSGGESDVEL EDYEVDDFRD GIVESRGNRF NPLTNFLGLD FAGGSGGKFT VINGIRDISR GSIVHPDNR WYKAWTMFIL IWALYSSFFT PLEFGFFRGL PENLFILDIA GQIAFLVDIV LTFFVAYRDS RTYRMIYKRS S IALRYLKS TFIIDLLACM PWDIIYKAAG EKEEVRYLLL IRLYRVHRVI LFFHKMEKDI RINYLFTRIV KLIFVELYCT HT AACIFYY LATTLPASQE GYTWIGSLKL GDYSYSKFRE IDLWTRYTTS MYFAVVTMAT VGYGDIHAVN MREMIFAMVY ISF DMILGA YLIGNMTALI VKGSKTERFR DKMADIMRYM NRNKLGRNIR GQITGHLRLQ YESSYTEAAV LQDIPVSIRA KIAQ TLYLP YIEKVPLFRG CSSEFINQIV IRLHEEFFLP GEVIMEQGSV VDQLYFVCHG VLEEIGITKD GSEEIVAVLQ PDHSF GEIS ILCNIPQPYT VRVAELCRIL RLDKQSFMNI LEIFFHDGRR ILNNLLEGKE SNVRIKQLES DITFHISKQE AELALK LNS AAFYGDLYQL KSLIRAGGDP NKTDYDGRSP LHLAASRGYE DITLYLIQES VDVNIKDKLG STPLLEAIKN GNDRVAA LL VKEGATLNIE NAGTFLCTVV AKGDSDFLKR LLSNGIDPNS KDYDHRTPLH VAASEGFYVL AIQLVEASAN VLAKDRWG N TPLDEALGCG NKMLIKLLED AKNSQISSFP SGSKEPKDKV YKKKCTVYFS HPGDSKEKRR RGIVLWVPRS IEELIRTAK EQLNVPEASC VLSEDEAKII DVDLISDGQK LYLAVET

UniProtKB: Potassium channel SKOR

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Macromolecule #2: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 2 / Number of copies: 15 / Formula: PC1
Molecular weightTheoretical: 790.145 Da
Chemical component information

ChemComp-PC1:
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / phospholipid*YM

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN 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: DIFFRACTION / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 153828
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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