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- EMDB-40350: CryoEM structure of rat Kv2.1(1-598) L403A mutant in nanodiscs -

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Basic information

Entry
Database: EMDB / ID: EMD-40350
TitleCryoEM structure of rat Kv2.1(1-598) L403A mutant in nanodiscs
Map data
Sample
  • Complex: Voltage-dependent potassium channel Kv2.1 L403A mutant
    • Protein or peptide: Potassium voltage-gated channel subfamily B member 1
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: POTASSIUM IONPotassium
Keywordsvoltage-dependent potassium channel / MEMBRANE PROTEIN
Function / homology
Function and homology information


regulation of action potential / clustering of voltage-gated potassium channels / positive regulation of long-term synaptic depression / regulation of motor neuron apoptotic process / Voltage gated Potassium channels / positive regulation of norepinephrine secretion / positive regulation of catecholamine secretion / potassium ion export across plasma membrane / proximal dendrite / positive regulation of calcium ion-dependent exocytosis ...regulation of action potential / clustering of voltage-gated potassium channels / positive regulation of long-term synaptic depression / regulation of motor neuron apoptotic process / Voltage gated Potassium channels / positive regulation of norepinephrine secretion / positive regulation of catecholamine secretion / potassium ion export across plasma membrane / proximal dendrite / positive regulation of calcium ion-dependent exocytosis / cholinergic synapse / delayed rectifier potassium channel activity / vesicle docking involved in exocytosis / outward rectifier potassium channel activity / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / postsynaptic specialization membrane / glutamate receptor signaling pathway / response to L-glutamate / action potential / neuronal cell body membrane / voltage-gated potassium channel activity / cellular response to nutrient levels / positive regulation of protein targeting to membrane / response to axon injury / negative regulation of insulin secretion / lateral plasma membrane / voltage-gated potassium channel complex / potassium ion transmembrane transport / dendrite membrane / cellular response to calcium ion / SNARE binding / protein localization to plasma membrane / cellular response to glucose stimulus / sarcolemma / protein homooligomerization / potassium ion transport / glucose homeostasis / perikaryon / postsynaptic membrane / transmembrane transporter binding / apical plasma membrane / protein heterodimerization activity / axon / neuronal cell body / dendrite / perinuclear region of cytoplasm / cell surface / plasma membrane
Similarity search - Function
Potassium channel, voltage dependent, Kv2.1 / Potassium channel, voltage dependent, Kv2 / Kv2 voltage-gated K+ channel / 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 ...Potassium channel, voltage dependent, Kv2.1 / Potassium channel, voltage dependent, Kv2 / Kv2 voltage-gated K+ channel / 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 subfamily B member 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.32 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: 2023
Title: Inactivation of the Kv2.1 channel through electromechanical coupling.
Authors: Ana I Fernández-Mariño / Xiao-Feng Tan / Chanhyung Bae / Kate Huffer / Jiansen Jiang / Kenton J Swartz /
Abstract: The Kv2.1 voltage-activated potassium (Kv) channel is a prominent delayed-rectifier Kv channel in the mammalian central nervous system, where its mechanisms of activation and inactivation are ...The Kv2.1 voltage-activated potassium (Kv) channel is a prominent delayed-rectifier Kv channel in the mammalian central nervous system, where its mechanisms of activation and inactivation are critical for regulating intrinsic neuronal excitability. Here we present structures of the Kv2.1 channel in a lipid environment using cryo-electron microscopy to provide a framework for exploring its functional mechanisms and how mutations causing epileptic encephalopathies alter channel activity. By studying a series of disease-causing mutations, we identified one that illuminates a hydrophobic coupling nexus near the internal end of the pore that is critical for inactivation. Both functional and structural studies reveal that inactivation in Kv2.1 results from dynamic alterations in electromechanical coupling to reposition pore-lining S6 helices and close the internal pore. Consideration of these findings along with available structures for other Kv channels, as well as voltage-activated sodium and calcium channels, suggests that related mechanisms of inactivation are conserved in voltage-activated cation channels and likely to be engaged by widely used therapeutics to achieve state-dependent regulation of channel activity.
History
DepositionApr 6, 2023-
Header (metadata) releaseSep 27, 2023-
Map releaseSep 27, 2023-
UpdateOct 25, 2023-
Current statusOct 25, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40350.png

Downloads & links

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Map

FileDownload / File: emd_40350.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.83 Å
Density
Contour LevelBy AUTHOR: 0.0055
Minimum - Maximum-0.024658183 - 0.048347063
Average (Standard dev.)0.00003028189 (±0.0010796072)
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: #2

Fileemd_40350_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_40350_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-dependent potassium channel Kv2.1 L403A mutant

EntireName: Voltage-dependent potassium channel Kv2.1 L403A mutant
Components
  • Complex: Voltage-dependent potassium channel Kv2.1 L403A mutant
    • Protein or peptide: Potassium voltage-gated channel subfamily B member 1
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: POTASSIUM IONPotassium

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Supramolecule #1: Voltage-dependent potassium channel Kv2.1 L403A mutant

SupramoleculeName: Voltage-dependent potassium channel Kv2.1 L403A mutant
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Rattus norvegicus (Norway rat)

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Macromolecule #1: Potassium voltage-gated channel subfamily B member 1

MacromoleculeName: Potassium voltage-gated channel subfamily B member 1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 68.550023 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GTMTKHGSRS TSSLPPEPME IVRSKACSRR VRLNVGGLAH EVLWRTLDRL PRTRLGKLRD CNTHDSLLQV CDDYSLEDNE YFFDRHPGA FTSILNFYRT GRLHMMEEMC ALSFSQELDY WGIDEIYLES CCQARYHQKK EQMNEELKRE AETLREREGE E FDNTCCAE ...String:
GTMTKHGSRS TSSLPPEPME IVRSKACSRR VRLNVGGLAH EVLWRTLDRL PRTRLGKLRD CNTHDSLLQV CDDYSLEDNE YFFDRHPGA FTSILNFYRT GRLHMMEEMC ALSFSQELDY WGIDEIYLES CCQARYHQKK EQMNEELKRE AETLREREGE E FDNTCCAE KRKKLWDLLE KPNSSVAAKI LAIISIMFIV LSTIALSLNT LPELQSLDEF GQSTDNPQLA HVEAVCIAWF TM EYLLRFL SSPKKWKFFK GPLNAIDLLA ILPYYVTIFL TESNKSVLQF QNVRRVVQIF RIMRILRILK LARHSTGLQS LGF TLRRSY NELGLLILFL AMGIMIFSSL VFFAEKDEDD TKFKSIPASF WWATITMTTV GYGDIYPKTL LGKIVGGLCC IAGV LVIAA PIPIIVNNFS EFYKEQKRQE KAIKRREALE RAKRNGSIVS MNMKDAFARS IEMMDIVVEK NGESIAKKDK VQDNH LSPN KWKWTKRALS ETSSSKSFET KEQGSPEKAR SSSSPQHLNV QQLEDMYSKM AKTQSQPILN TKEMAPQSKP PEELEM SSM PSPVAPLPAR TEGVIDMRSM SSIDSFISCA TDFPEAT

UniProtKB: Potassium voltage-gated channel subfamily B member 1

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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: 15 / 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 / POPC

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Macromolecule #3: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 3 / Number of copies: 4 / Formula: K
Molecular weightTheoretical: 39.098 Da

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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 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 48.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.32 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 505078

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-8sda:
CryoEM structure of rat Kv2.1(1-598) L403A mutant in nanodiscs

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