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- PDB-8vc4: Voltage gated potassium ion channel Kv1.2 in Sodium -

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Basic information

Entry
Database: PDB / ID: 8vc4
TitleVoltage gated potassium ion channel Kv1.2 in Sodium
ComponentsPotassium voltage-gated channel subfamily A member 2
KeywordsMEMBRANE PROTEIN / Ion Channel / Sodium bound
Function / homology
Function and homology information


optic nerve structural organization / Voltage gated Potassium channels / potassium channel complex / voltage-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / paranodal junction / potassium ion export across plasma membrane / regulation of circadian sleep/wake cycle, non-REM sleep / corpus callosum development / delayed rectifier potassium channel activity / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential ...optic nerve structural organization / Voltage gated Potassium channels / potassium channel complex / voltage-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / paranodal junction / potassium ion export across plasma membrane / regulation of circadian sleep/wake cycle, non-REM sleep / corpus callosum development / delayed rectifier potassium channel activity / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / axon initial segment / juxtaparanode region of axon / outward rectifier potassium channel activity / optic nerve development / neuronal cell body membrane / regulation of dopamine secretion / kinesin binding / lamellipodium membrane / voltage-gated potassium channel activity / action potential / neuronal action potential / voltage-gated potassium channel complex / axon terminus / sensory perception of pain / potassium ion transmembrane transport / calyx of Held / protein homooligomerization / cerebral cortex development / lamellipodium / presynaptic membrane / perikaryon / postsynaptic membrane / endosome / axon / dendrite / endoplasmic reticulum membrane / glutamatergic synapse / membrane / plasma membrane
Similarity search - Function
Potassium channel, voltage dependent, Kv1.2 / Potassium channel, voltage dependent, Kv1 / Potassium channel, voltage dependent, Kv / Potassium channel tetramerisation-type BTB domain / BTB/POZ domain / Voltage-gated potassium channel / Voltage-dependent channel domain superfamily / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / SKP1/BTB/POZ domain superfamily ...Potassium channel, voltage dependent, Kv1.2 / Potassium channel, voltage dependent, Kv1 / Potassium channel, voltage dependent, Kv / Potassium channel tetramerisation-type BTB domain / BTB/POZ domain / Voltage-gated potassium channel / Voltage-dependent channel domain superfamily / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / SKP1/BTB/POZ domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Potassium voltage-gated channel subfamily A member 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.17 Å
AuthorsWu, Y. / Sigworth, F.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Research Resources (NIH/NCRR)GR108615 United States
CitationJournal: bioRxiv / Year: 2024
Title: Cryo-EM structures of Kv1.2 potassium channels, conducting and non-conducting.
Authors: Yangyu Wu / Yangyang Yan / Youshan Yang / Shumin Bian / Alberto Rivetta / Ken Allen / Fred J Sigworth /
Abstract: We present near-atomic-resolution cryo-EM structures of the mammalian voltage-gated potassium channel Kv1.2 in open, C-type inactivated, toxin-blocked and sodium-bound states at 3.2 Å, 2.5 Å, 3.2 ...We present near-atomic-resolution cryo-EM structures of the mammalian voltage-gated potassium channel Kv1.2 in open, C-type inactivated, toxin-blocked and sodium-bound states at 3.2 Å, 2.5 Å, 3.2 Å, and 2.9Å. These structures, all obtained at nominally zero membrane potential in detergent micelles, reveal distinct ion-occupancy patterns in the selectivity filter. The first two structures are very similar to those reported in the related Shaker channel and the much-studied Kv1.2-2.1 chimeric channel. On the other hand, two new structures show unexpected patterns of ion occupancy. First, the toxin α-Dendrotoxin, like Charybdotoxin, is seen to attach to the negatively-charged channel outer mouth, and a lysine residue penetrates into the selectivity filter, with the terminal amine coordinated by carbonyls, partially disrupting the outermost ion-binding site. In the remainder of the filter two densities of bound ions are observed, rather than three as observed with other toxin-blocked Kv channels. Second, a structure of Kv1.2 in Na solution does not show collapse or destabilization of the selectivity filter, but instead shows an intact selectivity filter with ion density in each binding site. We also attempted to image the C-type inactivated Kv1.2 W366F channel in Na solution, but the protein conformation was seen to be highly variable and only a low-resolution structure could be obtained. These findings present new insights into the stability of the selectivity filter and the mechanism of toxin block of this intensively studied, voltage-gated potassium channel.
History
DepositionDec 13, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2024Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_abbrev / _citation.year ..._citation.journal_abbrev / _citation.year / _citation_author.identifier_ORCID / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Potassium voltage-gated channel subfamily A member 2
B: Potassium voltage-gated channel subfamily A member 2
C: Potassium voltage-gated channel subfamily A member 2
D: Potassium voltage-gated channel subfamily A member 2


Theoretical massNumber of molelcules
Total (without water)242,3664
Polymers242,3664
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Potassium voltage-gated channel subfamily A member 2


Mass: 60591.570 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Kcna2 / Production host: Komagataella pastoris (fungus) / References: UniProt: P63142

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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: Voltage gated potassium channel Kv1.2 in Sodium / Type: CELL / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Rattus norvegicus (Norway rat)
Source (recombinant)Organism: Komagataella pastoris (fungus) / Strain: SMD1168
Buffer solutionpH: 7.4
SpecimenConc.: 0.1 mg/ml / Embedding 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: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21rc1_5107: / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 336318 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 80.01 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00297936
ELECTRON MICROSCOPYf_angle_d0.582210808
ELECTRON MICROSCOPYf_chiral_restr0.03961288
ELECTRON MICROSCOPYf_plane_restr0.00511332
ELECTRON MICROSCOPYf_dihedral_angle_d3.83051084

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