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- EMDB-43136: Voltage gated potassium ion channel Kv1.2 W366F, C-type inactivated -

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Basic information

Entry
Database: EMDB / ID: EMD-43136
TitleVoltage gated potassium ion channel Kv1.2 W366F, C-type inactivated
Map data
Sample
  • Cell: Voltage gated potassium channel Kv1.2 W366F, C-type inactivated
    • Protein or peptide: Potassium voltage-gated channel subfamily A member 2
  • Ligand: POTASSIUM ION
KeywordsIon Channel / mutant / C-type inactivated / MEMBRANE PROTEIN
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 / regulation of circadian sleep/wake cycle, non-REM sleep / paranodal junction / potassium ion export across plasma membrane / corpus callosum development / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / delayed rectifier potassium channel activity ...optic nerve structural organization / Voltage gated Potassium channels / potassium channel complex / voltage-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / regulation of circadian sleep/wake cycle, non-REM sleep / paranodal junction / potassium ion export across plasma membrane / corpus callosum development / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / delayed rectifier potassium channel activity / axon initial segment / optic nerve development / juxtaparanode region of axon / outward rectifier potassium channel activity / neuronal cell body membrane / regulation of dopamine secretion / lamellipodium membrane / action potential / kinesin binding / voltage-gated potassium channel activity / neuronal action potential / voltage-gated potassium channel complex / axon terminus / potassium ion transmembrane transport / sensory perception of pain / 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 / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / Voltage-dependent channel domain superfamily / 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 / 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
Potassium voltage-gated channel subfamily A member 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.55 Å
AuthorsWu Y / Sigworth FJ
Funding support United States, 1 items
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 14, 2023-
Header (metadata) releaseJul 10, 2024-
Map releaseJul 10, 2024-
UpdateJul 17, 2024-
Current statusJul 17, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43136.png

Downloads & links

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Map

FileDownload / File: emd_43136.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 256 pix.
= 273.408 Å		1.07 Å/pix.
x 256 pix.
= 273.408 Å		1.07 Å/pix.
x 256 pix.
= 273.408 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.068 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0244
Minimum - Maximum-0.05659952 - 0.13265434
Average (Standard dev.)0.00016931137 (±0.0024433292)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 273.408 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_43136_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_43136_half_map_2.map
Projections & Slices
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Sample components

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Entire : Voltage gated potassium channel Kv1.2 W366F, C-type inactivated

EntireName: Voltage gated potassium channel Kv1.2 W366F, C-type inactivated
Components
  • Cell: Voltage gated potassium channel Kv1.2 W366F, C-type inactivated
    • Protein or peptide: Potassium voltage-gated channel subfamily A member 2
  • Ligand: POTASSIUM ION

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Supramolecule #1: Voltage gated potassium channel Kv1.2 W366F, C-type inactivated

SupramoleculeName: Voltage gated potassium channel Kv1.2 W366F, C-type inactivated
type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Rattus norvegicus (Norway rat)

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

MacromoleculeName: Potassium voltage-gated channel subfamily A member 2 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 60.552523 KDa
Recombinant expressionOrganism: Komagataella pastoris (fungus)
SequenceString: MSAWSHPQFE KGGGSGGGSG GSAWSHPQFE KLVPRGSMTV ATGDPVDEAA AHPGHPQDTY DPEADHECCE RVVINISGLR FETQLKTLA QFPETLLGDP KKRMRYFDPL RNEYFFDRNR PSFDAILYYY QSGGRLRRPV NVPLDIFSEE IRFYELGEEA M EMFREDEG ...String:
MSAWSHPQFE KGGGSGGGSG GSAWSHPQFE KLVPRGSMTV ATGDPVDEAA AHPGHPQDTY DPEADHECCE RVVINISGLR FETQLKTLA QFPETLLGDP KKRMRYFDPL RNEYFFDRNR PSFDAILYYY QSGGRLRRPV NVPLDIFSEE IRFYELGEEA M EMFREDEG YIKEEERPLP ENEFQRQVWL LFEYPESSGP ARIIAIVSVM VILISIVSFC LETLPIFRDE NEDMHGSGVT FH TYSQSTI GYQQSTSFTD PFFIVETLCI IWFSFEFLVR FFACPSKAGF FTNIMNIIDI VAIIPYFITL GTELAEKPED AQQ GQQAMS LAILRVIRLV RVFRIFKLSR HSKGLQILGQ TLKASMRELG LLIFFLFIGV ILFSSAVYFA EADERDSQFP SIPD AFFWA VVSMTTVGYG DMVPTTIGGK IVGSLCAIAG VLTIALPVPV IVSNFNYFYH RETEGEEQAQ YLQVTSCPKI PSSPD LKKS RSASTISKSD YMEIQEGVNN SNEDFREENL KTANCTLANT NYVNITKMLT DV

UniProtKB: Potassium voltage-gated channel subfamily A member 2

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Macromolecule #2: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: K
Molecular weightTheoretical: 39.098 Da

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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

Concentration0.1 mg/mL
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: 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.55 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 266495
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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