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- EMDB-49308: AcA-EI-shaker Class C -

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Basic information

Entry
Database: EMDB / ID: EMD-49308
TitleAcA-EI-shaker Class C
Map data
Sample
  • Cell: voltage-gated potassium channel Shaker D12KE13K mutant
    • Protein or peptide: Potassium voltage-gated channel protein Shaker
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: POTASSIUM ION
  • Ligand: water
Keywordsvoltage-gated potassium channel / MEMBRANE PROTEIN
Function / homology
Function and homology information


mating behavior, sex discrimination / Phase 3 - rapid repolarisation / behavioral response to ether / Voltage gated Potassium channels / proboscis extension reflex / larval locomotory behavior / regulation of synaptic activity / courtship behavior / positive regulation of membrane potential / regulation of circadian sleep/wake cycle, sleep ...mating behavior, sex discrimination / Phase 3 - rapid repolarisation / behavioral response to ether / Voltage gated Potassium channels / proboscis extension reflex / larval locomotory behavior / regulation of synaptic activity / courtship behavior / positive regulation of membrane potential / regulation of circadian sleep/wake cycle, sleep / positive regulation of circadian sleep/wake cycle, sleep / detection of visible light / delayed rectifier potassium channel activity / cellular response to dopamine / sleep / axon extension / voltage-gated monoatomic cation channel activity / action potential / voltage-gated potassium channel activity / voltage-gated potassium channel complex / potassium ion transmembrane transport / protein homooligomerization / potassium ion transport / sensory perception of taste / perikaryon / learning or memory / neuron projection / membrane raft / membrane
Similarity search - Function
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 protein Shaker
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.17 Å
AuthorsTan X / Swartz KJ
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS) United States
CitationJournal: Nature / Year: 2025
Title: Structural basis of fast N-type inactivation in K channels.
Authors: Xiao-Feng Tan / Ana I Fernández-Mariño / Yan Li / Tsg-Hui Chang / Kenton J Swartz /
Abstract: Action potentials are generated by opening of voltage-activated sodium (Na) and potassium (K) channels, which can rapidly inactivate to shape the nerve impulse and contribute to synaptic facilitation ...Action potentials are generated by opening of voltage-activated sodium (Na) and potassium (K) channels, which can rapidly inactivate to shape the nerve impulse and contribute to synaptic facilitation and short-term memory. The mechanism of fast inactivation was proposed to involve an intracellular domain that blocks the internal pore in both Na and K channels; however, recent studies in Na and K channels support a mechanism in which the internal pore closes during inactivation. Here we investigate the mechanism of fast inactivation in the Shaker K channel using cryo-electron microscopy, mass spectrometry and electrophysiology. We resolved structures of a fully inactivated state in which the non-polar end of the N terminus plugs the internal pore in an extended conformation. The N-terminal methionine is deleted, leaving an alanine that is acetylated and interacts with a pore-lining isoleucine residue where RNA editing regulates fast inactivation. Opening of the internal activation gate is required for fast inactivation because it enables the plug domain to block the pore and repositions gate residues to interact with and stabilize that domain. We also show that external K destabilizes the inactivated state by altering the conformation of the ion selectivity filter rather than by electrostatic repulsion. These findings establish the mechanism of fast inactivation in K channels, revealing how it is regulated by RNA editing and N-terminal acetylation, and providing a framework for understanding related mechanisms in other voltage-activated channels.
History
DepositionFeb 19, 2025-
Header (metadata) releaseAug 6, 2025-
Map releaseAug 6, 2025-
UpdateOct 8, 2025-
Current statusOct 8, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49308.png

Downloads & links

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Map

FileDownload / File: emd_49308.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 300 pix.
= 249. Å		0.83 Å/pix.
x 300 pix.
= 249. Å		0.83 Å/pix.
x 300 pix.
= 249. Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.2928054 - 0.58532697
Average (Standard dev.)0.00024874217 (±0.017535413)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 249.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_49308_msk_1.map
Projections & Slices
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Histogram

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Half map: #2

Fileemd_49308_half_map_1.map
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Half map: #1

Fileemd_49308_half_map_2.map
Projections & Slices
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Sample components

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Entire : voltage-gated potassium channel Shaker D12KE13K mutant

EntireName: voltage-gated potassium channel Shaker D12KE13K mutant
Components
  • Cell: voltage-gated potassium channel Shaker D12KE13K mutant
    • Protein or peptide: Potassium voltage-gated channel protein Shaker
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: POTASSIUM ION
  • Ligand: water

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Supramolecule #1: voltage-gated potassium channel Shaker D12KE13K mutant

SupramoleculeName: voltage-gated potassium channel Shaker D12KE13K mutant
type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Drosophila melanogaster (fruit fly)

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Macromolecule #1: Potassium voltage-gated channel protein Shaker

MacromoleculeName: Potassium voltage-gated channel protein Shaker / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 75.474023 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: (ACE)AAVAGLYGL GKKRQHRKKQ QQQQQHQKEQ LEQKEEQKKI AERKLQLREQ QLQRNSLDGY GSLPKLSSQD EEGGAG HGF GGGPQHFEPI PHDHDFCERV VINVSGLRFE TQLRTLNQFP DTLLGDPARR LRYFDPLRNE YFFDRSRPSF DAILYYY QS GGRLRRPVNV ...String:
(ACE)AAVAGLYGL GKKRQHRKKQ QQQQQHQKEQ LEQKEEQKKI AERKLQLREQ QLQRNSLDGY GSLPKLSSQD EEGGAG HGF GGGPQHFEPI PHDHDFCERV VINVSGLRFE TQLRTLNQFP DTLLGDPARR LRYFDPLRNE YFFDRSRPSF DAILYYY QS GGRLRRPVNV PLDVFSEEIK FYELGDQAIN KFREDEGFIK EEERPLPDNE KQRKVWLLFE YPESSQAARV VAIISVFV I LLSIVIFCLE TLPEFKHYKV FNTTTNGTKI EEDEVPDITD PFFLIETLCI IWFTFELTVR FLACPNKLNF CRDVMNVID IIAIIPYFIT LATVVAEEED TLNLPKAPVS PQDKSSNQAM SLAILRVIRL VRVFRIFKLS RHSKGLQILG RTLKASMREL GLLIFFLFI GVVLFSSAVY FAEAGSENSF FKSIPDAFWW AVVTMTTVGY GDMTPVGVWG KIVGSLCAIA GVLTIALPVP V IVSNFNYF YHRETDQEEM QSQNFNHVTS CPYLPGTLVG QHMKKSSLSE SSSDMMDLDD GVESTPGLTE THPGRSAVAP FL GAQQQQQ QPVASSLSMS IDKQLQHPLQ QLTQTQLYQQ QQQQQQQQQN GFKQQQQQTQ QQLQQQQSHT INASAAAATS GSG SSGLTM RHNNALAVSI ETDVGSGGGS ENLYFQ

UniProtKB: Potassium voltage-gated channel protein Shaker

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Macromolecule #2: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...

MacromoleculeName: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
type: ligand / ID: 2 / Number of copies: 32 / Formula: POV
Molecular weightTheoretical: 760.076 Da
Chemical component information

ChemComp-POV:
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / phospholipid*YM

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Macromolecule #3: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: K
Molecular weightTheoretical: 39.098 Da

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 1 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration3 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
46.0 mMNaClsodium chloride
4.0 mMKClpotassium chloride
20.0 mMTris-Cltris(hydroxymethyl)aminomethane hydrochloride
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 289 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 90434
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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