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- PDB-7ej1: human voltage-gated potassium channel KV1.3 -

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Basic information

Entry
Database: PDB / ID: 7ej1
Titlehuman voltage-gated potassium channel KV1.3
Components
  • Potassium voltage-gated channel subfamily A member 3
  • Voltage-gated potassium channel subunit beta-2
KeywordsMEMBRANE PROTEIN / potassium channel / complex
Function / homology
Function and homology information


pinceau fiber / methylglyoxal reductase (NADPH) (acetol producing) activity / regulation of protein localization to cell surface / voltage-gated monoatomic ion channel activity / : / delayed rectifier potassium channel activity / Voltage gated Potassium channels / juxtaparanode region of axon / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / regulation of potassium ion transmembrane transport ...pinceau fiber / methylglyoxal reductase (NADPH) (acetol producing) activity / regulation of protein localization to cell surface / voltage-gated monoatomic ion channel activity / : / delayed rectifier potassium channel activity / Voltage gated Potassium channels / juxtaparanode region of axon / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / regulation of potassium ion transmembrane transport / tertiary granule membrane / action potential / voltage-gated potassium channel activity / potassium channel regulator activity / specific granule membrane / voltage-gated potassium channel complex / potassium ion transmembrane transport / protein homooligomerization / potassium ion transport / cytoplasmic side of plasma membrane / transmembrane transporter binding / cytoskeleton / axon / synapse / Neutrophil degranulation / perinuclear region of cytoplasm / membrane / plasma membrane / cytosol
Similarity search - Function
Potassium channel, voltage dependent, Kv1.3 / Potassium channel, voltage-dependent, beta subunit, KCNAB2 / Potassium channel, voltage-dependent, beta subunit, KCNAB / Potassium channel, voltage-dependent, beta subunit, KCNAB-related / Potassium channel, voltage dependent, Kv1 / Potassium channel, voltage dependent, Kv / Potassium channel tetramerisation-type BTB domain / BTB/POZ domain / Voltage-gated potassium channel / NADP-dependent oxidoreductase domain ...Potassium channel, voltage dependent, Kv1.3 / Potassium channel, voltage-dependent, beta subunit, KCNAB2 / Potassium channel, voltage-dependent, beta subunit, KCNAB / Potassium channel, voltage-dependent, beta subunit, KCNAB-related / Potassium channel, voltage dependent, Kv1 / Potassium channel, voltage dependent, Kv / Potassium channel tetramerisation-type BTB domain / BTB/POZ domain / Voltage-gated potassium channel / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / Voltage-dependent channel domain superfamily / SKP1/BTB/POZ domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Potassium voltage-gated channel subfamily A member 3 / Voltage-gated potassium channel subunit beta-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsLiu, S. / Zhao, Y. / Tian, C.
CitationJournal: Cell Discov / Year: 2021
Title: Structures of wild-type and H451N mutant human lymphocyte potassium channel K1.3.
Authors: Sanling Liu / Yue Zhao / Hao Dong / Liang Xiao / Yong Zhang / Yuqin Yang / Seow Theng Ong / K George Chandy / Longhua Zhang / Changlin Tian /
History
DepositionApr 1, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
A: Voltage-gated potassium channel subunit beta-2
B: Potassium voltage-gated channel subfamily A member 3
C: Voltage-gated potassium channel subunit beta-2
D: Potassium voltage-gated channel subfamily A member 3
E: Voltage-gated potassium channel subunit beta-2
F: Potassium voltage-gated channel subfamily A member 3
G: Voltage-gated potassium channel subunit beta-2
H: Potassium voltage-gated channel subfamily A member 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)422,79612
Polymers419,8238
Non-polymers2,9744
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area33330 Å2
ΔGint-187 kcal/mol
Surface area120260 Å2

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Components

#1: Protein
Voltage-gated potassium channel subunit beta-2 / K(+) channel subunit beta-2 / Kv-beta-2 / hKvbeta2


Mass: 41049.152 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KCNAB2, KCNA2B, KCNK2 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q13303, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#2: Protein
Potassium voltage-gated channel subfamily A member 3 / HGK5 / HLK3 / HPCN3 / Voltage-gated K(+) channel HuKIII / Voltage-gated potassium channel subunit Kv1.3


Mass: 63906.480 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KCNA3, HGK5 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P22001
#3: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
Has ligand of interestN

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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: Human potassium channel KV1.3/KVb2.1 complex / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
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
Image recordingElectron dose: 62 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.17.1_3660refinement
PHENIX1.17.1_3660refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 Å / Num. of particles: 44078 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 89.91 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.009321728
ELECTRON MICROSCOPYf_angle_d0.916429532
ELECTRON MICROSCOPYf_chiral_restr0.05513344
ELECTRON MICROSCOPYf_plane_restr0.00693728
ELECTRON MICROSCOPYf_dihedral_angle_d18.31047704

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