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- EMDB-49305: AcA-EI-shaker with free peptide conformation A -

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Basic information

Entry
Database: EMDB / ID: EMD-49305
TitleAcA-EI-shaker with free peptide conformation A
Map data
Sample
  • Cell: voltage-gated potassium channel Shaker
    • 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 / sleep / cellular response to dopamine / 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 / Voltage-dependent channel domain superfamily / BTB/POZ domain / 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: 3.2 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 Kv channels
Authors: Tan X / Fernandez-Marino AI / Li Y / Chang T-H / Swartz KJ
History
DepositionFeb 19, 2025-
Header (metadata) releaseAug 6, 2025-
Map releaseAug 6, 2025-
UpdateAug 6, 2025-
Current statusAug 6, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49305.png

Downloads & links

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Map

FileDownload / File: emd_49305.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

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-0.8576584 - 1.3935981
Average (Standard dev.)-0.0017669993 (±0.040789526)
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_49305_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_49305_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_49305_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : voltage-gated potassium channel Shaker

EntireName: voltage-gated potassium channel Shaker
Components
  • Cell: voltage-gated potassium channel Shaker
    • 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

SupramoleculeName: voltage-gated potassium channel Shaker / 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

Concentration4.5 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: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 109792
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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