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- PDB-8jet: Conformation 1 of the plant potassium channel SKOR -

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Basic information

Entry
Database: PDB / ID: 8jet
TitleConformation 1 of the plant potassium channel SKOR
ComponentsPotassium channel SKOR
KeywordsPLANT PROTEIN / voltage-gated potassium channel / outward-rectifier / symmetry reduction / ploy-ankyrin domain
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsLiu, S. / Li, S. / Sun, D. / Tian, C.
Funding support China, 2items
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, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Potassium channel SKOR
B: Potassium channel SKOR
C: Potassium channel SKOR
D: Potassium channel SKOR


Theoretical massNumber of molelcules
Total (without water)376,0444
Polymers376,0444
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Potassium channel SKOR / Stelar K(+) outward rectifying channel


Mass: 94011.062 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SKOR, At3g02850, F13E7.21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9M8S6

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Tetrameric SKOR complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 56 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.20.1_4487refinement
PHENIX1.20.1_4487refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 129992 / Symmetry type: POINT
RefinementCross valid method: NONE
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.001619952
ELECTRON MICROSCOPYf_angle_d0.402727168
ELECTRON MICROSCOPYf_chiral_restr0.0373182
ELECTRON MICROSCOPYf_plane_restr0.00283430
ELECTRON MICROSCOPYf_dihedral_angle_d9.63946792

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