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- EMDB-49356: AcA-EI-shaker Class A -

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Basic information

Entry
Database: EMDB / ID: EMD-49356
TitleAcA-EI-shaker Class A
Map data
Sample
  • Cell: voltage-gated potassium channel Shaker D12KE13K mutant
    • Protein or peptide: Potassium voltage-gated channel Shaker E12KD13K mutant
Keywordsvoltage-gated potassium channel / MEMBRANE PROTEIN
Biological speciesDrosophila melanogaster (fruit fly)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.92 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 21, 2025-
Header (metadata) releaseDec 31, 2025-
Map releaseDec 31, 2025-
UpdateJul 15, 2026-
Current statusJul 15, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49356.png

Downloads & links

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Map

FileDownload / File: emd_49356.map.gz / Format: CCP4 / Size: 103 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.)
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: 0.126
Minimum - Maximum-0.45084637 - 0.6875161
Average (Standard dev.)0.0001489022 (±0.01943732)
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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Half map: #1

Fileemd_49356_half_map_1.map
Projections & Slices
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Density Histograms

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Histogram (log scale)

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Half map: #2

Fileemd_49356_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 Shaker E12KD13K mutant

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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: all
Source (natural)Organism: Drosophila melanogaster (fruit fly)

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Macromolecule #1: Potassium voltage-gated channel Shaker E12KD13K mutant

MacromoleculeName: Potassium voltage-gated channel Shaker E12KD13K mutant
type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: (ACE)AAVAGLYGL GKKRQHRKKQ QQQQQHQKEQ LEQKEEQKKI AERKLQLREQ QLQRNSLDGY GSLPKLSSQD EEGGAGHGFG GGPQHFEPIP HDHDFCERVV INVSGLRFET QLRTLNQFPD TLLGDPARRL RYFDPLRNEY FFDRSRPSFD AILYYYQSGG RLRRPVNVPL ...String:
(ACE)AAVAGLYGL GKKRQHRKKQ QQQQQHQKEQ LEQKEEQKKI AERKLQLREQ QLQRNSLDGY GSLPKLSSQD EEGGAGHGFG GGPQHFEPIP HDHDFCERVV INVSGLRFET QLRTLNQFPD TLLGDPARRL RYFDPLRNEY FFDRSRPSFD AILYYYQSGG RLRRPVNVPL DVFSEEIKFY ELGDQAINKF REDEGFIKEE ERPLPDNEKQ RKVWLLFEYP ESSQAARVVA IISVFVILLS IVIFCLETLP EFKHYKVFNT TTNGTKIEED EVPDITDPFF LIETLCIIWF TFELTVRFLA CPNKLNFCRD VMNVIDIIAI IPYFITLATV VAEEEDTLNL PKAPVSPQDK SSNQAMSLAI LRVIRLVRVF RIFKLSRHSK GLQILGRTLK ASMRELGLLI FFLFIGVVLF SSAVYFAEAG SENSFFKSIP DAFWWAVVTM TTVGYGDMTP VGVWGKIVGS LCAIAGVLTI ALPVPVIVSN FNYFYHRETD QEEMQSQNFN HVTSCPYLPG TLVGQHMKKS SLSESSSDMM DLDDGVESTP GLTETHPGRS AVAPFLGAQQ QQQQPVASSL SMSIDKQLQH PLQQLTQTQL YQQQQQQQQQ QQNGFKQQQQ QTQQQLQQQQ SHTINASAAA ATSGSGSSGL TMRHNNALAV SIETDVGSGG GSENLYFQ

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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: 2.92 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 100375
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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