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- EMDB-43133: Voltage gated potassium ion channel Kv1.2 in Sodium -

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Basic information

Entry
Database: EMDB / ID: EMD-43133
TitleVoltage gated potassium ion channel Kv1.2 in Sodium
Map data
Sample
  • Cell: Voltage gated potassium channel Kv1.2 in Sodium
    • Protein or peptide: Potassium voltage-gated channel subfamily A member 2
KeywordsIon Channel / Sodium bound / 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 / 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 / lamellipodium membrane / kinesin binding / voltage-gated potassium channel activity / action potential / neuronal action potential / voltage-gated potassium channel complex / sensory perception of pain / axon terminus / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.17 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 13, 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_43133.png

Downloads & links

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Map

FileDownload / File: emd_43133.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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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
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Histogram (log scale)
Contour LevelBy AUTHOR: 1.1
Minimum - Maximum-8.596888 - 15.681264000000001
Average (Standard dev.)0.0022560381 (±0.19070812)
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: #1

Fileemd_43133_half_map_1.map
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Half map: #2

Fileemd_43133_half_map_2.map
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Sample components

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Entire : Voltage gated potassium channel Kv1.2 in Sodium

EntireName: Voltage gated potassium channel Kv1.2 in Sodium
Components
  • Cell: Voltage gated potassium channel Kv1.2 in Sodium
    • Protein or peptide: Potassium voltage-gated channel subfamily A member 2

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Supramolecule #1: Voltage gated potassium channel Kv1.2 in Sodium

SupramoleculeName: Voltage gated potassium channel Kv1.2 in Sodium / type: cell / ID: 1 / Parent: 0 / Macromolecule list: all
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: 60.59157 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 AFWWA 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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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: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 336318
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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