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- EMDB-25152: Structure of shaker-W434F -

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Basic information

Entry
Database: EMDB / ID: EMD-25152
TitleStructure of shaker-W434F
Map data
Sample
  • Cell: potassium channel
    • 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
Keywordspotassium 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 / positive 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 / positive regulation of circadian sleep/wake cycle, sleep / regulation of circadian sleep/wake cycle, sleep / detection of visible light / voltage-gated monoatomic cation channel activity / sleep / cellular response to dopamine / delayed rectifier potassium channel activity / axon extension / action potential / voltage-gated potassium channel activity / potassium ion transmembrane transport / voltage-gated potassium channel complex / potassium ion transport / protein homooligomerization / 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 / 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: 2.9 Å
AuthorsTan X / Bae C
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS) United States
CitationJournal: Sci Adv / Year: 2022
Title: Structure of the Shaker Kv channel and mechanism of slow C-type inactivation.
Authors: Xiao-Feng Tan / Chanhyung Bae / Robyn Stix / Ana I Fernández-Mariño / Kate Huffer / Tsg-Hui Chang / Jiansen Jiang / José D Faraldo-Gómez / Kenton J Swartz /
Abstract: Voltage-activated potassium (Kv) channels open upon membrane depolarization and proceed to spontaneously inactivate. Inactivation controls neuronal firing rates and serves as a form of short-term ...Voltage-activated potassium (Kv) channels open upon membrane depolarization and proceed to spontaneously inactivate. Inactivation controls neuronal firing rates and serves as a form of short-term memory and is implicated in various human neurological disorders. Here, we use high-resolution cryo-electron microscopy and computer simulations to determine one of the molecular mechanisms underlying this physiologically crucial process. Structures of the activated Shaker Kv channel and of its W434F mutant in lipid bilayers demonstrate that C-type inactivation entails the dilation of the ion selectivity filter and the repositioning of neighboring residues known to be functionally critical. Microsecond-scale molecular dynamics trajectories confirm that these changes inhibit rapid ion permeation through the channel. This long-sought breakthrough establishes how eukaryotic K channels self-regulate their functional state through the plasticity of their selectivity filters.
History
DepositionOct 15, 2021-
Header (metadata) releaseMar 30, 2022-
Map releaseMar 30, 2022-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_25152.png

Downloads & links

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Map

FileDownload / File: emd_25152.map.gz / Format: CCP4 / Size: 98.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.86 Å
Density
Contour LevelBy AUTHOR: 0.011
Minimum - Maximum-0.09635509 - 0.12978798
Average (Standard dev.)-0.0000050747212 (±0.0026279825)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions296296296
Spacing296296296
CellA=B=C: 254.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : potassium channel

EntireName: potassium channel
Components
  • Cell: potassium channel
    • 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: potassium channel

SupramoleculeName: potassium channel / 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: 4 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 69.436281 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GTMAAVALRE QQLQRNSLDG YGSLPKLSSQ DEEGGAGHGF GGGPQHFEPI PHDHDFCERV VINVSGLRFE TQLRTLNQFP DTLLGDPAR RLRYFDPLRN EYFFDRSRPS FDAILYYYQS GGRLRRPVNV PLDVFSEEIK FYELGDQAIN KFREDEGFIK E EERPLPDN ...String:
GTMAAVALRE QQLQRNSLDG YGSLPKLSSQ DEEGGAGHGF GGGPQHFEPI PHDHDFCERV VINVSGLRFE TQLRTLNQFP DTLLGDPAR RLRYFDPLRN EYFFDRSRPS FDAILYYYQS GGRLRRPVNV PLDVFSEEIK FYELGDQAIN KFREDEGFIK E EERPLPDN EKQRKVWLLF EYPESSQAAR VVAIISVFVI LLSIVIFCLE TLPEFKHYKV FNTTTNGTKI EEDEVPDITD PF FLIETLC IIWFTFELTV RFLACPNKLN FCRDVMNVID IIAIIPYFIT LATVVAEEED TLNLPKAPVS PQDKSSNQAM SLA ILRVIR LVRVFRIFKL SRHSKGLQIL GRTLKASMRE LGLLIFFLFI GVVLFSSAVY FAEAGSENSF FKSIPDAFFW AVVT MTTVG YGDMTPVGVW GKIVGSLCAI AGVLTIALPV PVIVSNFNYF YHRETDQEEM QSQNFNHVTS CPYLPGTLVG QHMKK SSLS ESSSDMMDLD DGVESTPGLT ETHPGRSAVA PFLGAQQQQQ QPVASSLSMS IDKQLQHPLQ QLTQTQLYQQ QQQQQQ QQQ NGFKQQQQQT QQQLQQQQSH TINASAAAAT SGSGSSGLTM RHNNALAVSI ETDV

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

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 16 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 212083
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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