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

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Basic information

Entry
Database: PDB / ID: 8sd3
TitleCryoEM structure of rat Kv2.1(1-598) wild type 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 / regulation of motor neuron apoptotic process / Voltage gated Potassium channels / clustering of voltage-gated potassium channels / positive regulation of long-term synaptic depression / positive regulation of norepinephrine secretion / positive regulation of catecholamine secretion / cholinergic synapse / potassium ion export across plasma membrane / positive regulation of calcium ion-dependent exocytosis ...regulation of action potential / regulation of motor neuron apoptotic process / Voltage gated Potassium channels / clustering of voltage-gated potassium channels / positive regulation of long-term synaptic depression / positive regulation of norepinephrine secretion / positive regulation of catecholamine secretion / cholinergic synapse / potassium ion export across plasma membrane / positive regulation of calcium ion-dependent exocytosis / proximal dendrite / delayed rectifier potassium channel activity / outward rectifier potassium channel activity / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / vesicle docking involved in exocytosis / response to L-glutamate / postsynaptic specialization membrane / neuronal cell body membrane / glutamate receptor signaling pathway / action potential / lateral plasma membrane / positive regulation of protein targeting to membrane / voltage-gated potassium channel activity / potassium channel regulator activity / response to axon injury / cellular response to nutrient levels / 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 / negative regulation of insulin secretion / sarcolemma / protein homooligomerization / potassium ion transport / glucose homeostasis / perikaryon / transmembrane transporter binding / postsynaptic membrane / 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 / Voltage-gated potassium channel / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / Voltage-dependent channel 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 / Voltage-gated potassium channel / 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: 2.95 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
C: Potassium voltage-gated channel subfamily B member 1
D: Potassium voltage-gated channel subfamily B member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)292,76732
Polymers274,3684
Non-polymers18,39828
Water00
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: 68592.102 Da / Num. of mol.: 4
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


Mass: 760.076 Da / Num. of mol.: 24 / 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 / 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
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
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 FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 71 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k 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: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 73548 / 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: 64.33 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00927972
ELECTRON MICROSCOPYf_angle_d0.72510752
ELECTRON MICROSCOPYf_chiral_restr0.04311264
ELECTRON MICROSCOPYf_plane_restr0.00541264
ELECTRON MICROSCOPYf_dihedral_angle_d18.7393008

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