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- EMDB-40349: CryoEM structure of rat Kv2.1(1-598) wild type in nanodiscs -

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Basic information

Entry
Database: EMDB / ID: EMD-40349
TitleCryoEM structure of rat Kv2.1(1-598) wild type in nanodiscs
Map data
Sample
  • Complex: Voltage-dependent potassium channel Kv2.1
    • 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 ION
Keywordsvoltage-dependent potassium channel / MEMBRANE PROTEIN
Function / homology
Function and homology information


regulation of action potential / positive regulation of long-term synaptic depression / regulation of motor neuron apoptotic process / clustering of voltage-gated potassium channels / Voltage gated Potassium channels / positive regulation of norepinephrine secretion / positive regulation of catecholamine secretion / positive regulation of calcium ion-dependent exocytosis / potassium ion export across plasma membrane / cholinergic synapse ...regulation of action potential / positive regulation of long-term synaptic depression / regulation of motor neuron apoptotic process / clustering of voltage-gated potassium channels / Voltage gated Potassium channels / positive regulation of norepinephrine secretion / positive regulation of catecholamine secretion / positive regulation of calcium ion-dependent exocytosis / potassium ion export across plasma membrane / cholinergic synapse / proximal dendrite / delayed rectifier potassium channel activity / outward rectifier potassium channel activity / vesicle docking involved in exocytosis / 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 / lateral plasma membrane / positive regulation of protein targeting to membrane / response to axon injury / negative regulation of insulin secretion / cellular response to nutrient levels / voltage-gated potassium channel complex / dendrite membrane / potassium ion transmembrane transport / cellular response to calcium ion / SNARE binding / protein localization to plasma membrane / cellular response to glucose stimulus / potassium ion transport / protein homooligomerization / sarcolemma / glucose homeostasis / perikaryon / postsynaptic membrane / transmembrane transporter binding / protein heterodimerization activity / apical plasma membrane / 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: 2.95 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_40349.png

Downloads & links

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Map

FileDownload / File: emd_40349.map.gz / Format: CCP4 / Size: 52.7 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.)
1.06 Å/pix.
x 240 pix.
= 254.4 Å		1.06 Å/pix.
x 240 pix.
= 254.4 Å		1.06 Å/pix.
x 240 pix.
= 254.4 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.026
Minimum - Maximum-0.13739106 - 0.26275292
Average (Standard dev.)0.00008119748 (±0.006488338)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 254.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_40349_half_map_1.map
Projections & Slices
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Slices (1/2)
Density Histograms

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Histogram (log scale)

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Half map: #1

Fileemd_40349_half_map_2.map
Projections & Slices
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Sample components

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Entire : Voltage-dependent potassium channel Kv2.1

EntireName: Voltage-dependent potassium channel Kv2.1
Components
  • Complex: Voltage-dependent potassium channel Kv2.1
    • 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 ION

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

SupramoleculeName: Voltage-dependent potassium channel Kv2.1 / 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: 68.592102 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 LVIAL 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: 24 / 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: 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
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 71.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 73548
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-8sd3:
CryoEM structure of rat Kv2.1(1-598) wild type in nanodiscs

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