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

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Basic information

Entry
Database: PDB / ID: 8sda
TitleCryoEM structure of rat Kv2.1(1-598) L403A mutant in nanodiscs
ComponentsPotassium voltage-gated channel subfamily B member 1
KeywordsMEMBRANE PROTEIN / voltage-dependent potassium channel
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
: / Chem-POV / Potassium voltage-gated channel subfamily B member 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.32 Å
AuthorsTan, X. / Swartz, K.J.
Funding support United States, 1items
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, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Oct 25, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Potassium voltage-gated channel subfamily B member 1
B: Potassium voltage-gated channel subfamily B member 1
D: Potassium voltage-gated channel subfamily B member 1
C: Potassium voltage-gated channel subfamily B member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)285,75823
Polymers274,2004
Non-polymers11,55819
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Potassium voltage-gated channel subfamily B member 1 / Delayed rectifier potassium channel 1 / DRK1 / Voltage-gated potassium channel subunit Kv2.1


Mass: 68550.023 Da / Num. of mol.: 4 / Mutation: L403A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Kcnb1 / Cell line (production host): HEK / Production host: Homo sapiens (human) / Strain (production host): TSA201 / References: UniProt: P15387
#2: Chemical
ChemComp-POV / (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / POPC / POPC


Mass: 760.076 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C42H82NO8P / Comment: phospholipid*YM
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Voltage-dependent potassium channel Kv2.1 L403A mutant
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Rattus norvegicus (Norway rat)
Source (recombinant)Organism: Homo sapiens (human) / Cell: tsa201
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: TUNGSTEN HAIRPIN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 48 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.19.1_4122refinement
PHENIX1.19.1_4122refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.32 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 505078 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 73.61 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00587550
ELECTRON MICROSCOPYf_angle_d0.736810235
ELECTRON MICROSCOPYf_chiral_restr0.04221245
ELECTRON MICROSCOPYf_plane_restr0.00481217
ELECTRON MICROSCOPYf_dihedral_angle_d14.25522715

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