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- PDB-9o12: Kv2.1 in an intermediate conformation with 2 voltage sensors down... -

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Basic information

Entry
Database: PDB / ID: 9o12
TitleKv2.1 in an intermediate conformation with 2 voltage sensors down and an open pore
ComponentsPotassium voltage-gated channel subfamily B member 1
KeywordsMEMBRANE PROTEIN / voltage-gated potassium channel
Function / homology
Function and homology information


regulation of action potential / regulation of motor neuron apoptotic process / 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 / delayed rectifier potassium channel activity ...regulation of action potential / regulation of motor neuron apoptotic process / 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 / delayed rectifier potassium channel activity / proximal dendrite / Voltage gated Potassium channels / outward rectifier potassium channel activity / 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 / 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 / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / glucose homeostasis / perikaryon / transmembrane transporter binding / postsynaptic membrane / apical plasma membrane / protein heterodimerization activity / axon / 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 / Voltage-dependent channel domain superfamily / BTB/POZ domain ...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 / Voltage-dependent channel domain superfamily / BTB/POZ domain / 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 speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsMandala, V.S. / MacKinnon, R.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: Electric field-induced pore constriction in the human K2.1 channel.
Authors: Venkata Shiva Mandala / Roderick MacKinnon /
Abstract: Gating in voltage-dependent ion channels is regulated by the transmembrane voltage. This form of regulation is enabled by voltage-sensing domains (VSDs) that respond to transmembrane voltage ...Gating in voltage-dependent ion channels is regulated by the transmembrane voltage. This form of regulation is enabled by voltage-sensing domains (VSDs) that respond to transmembrane voltage differences by changing their conformation and exerting force on the pore to open or close it. Here, we use cryogenic electron microscopy to study the neuronal K2.1 channel in lipid vesicles with and without a voltage difference across the membrane. Hyperpolarizing voltage differences displace the positively charged S4 helix in the voltage sensor by one helical turn (~5 Å). When this displacement occurs, the S4 helix changes its contact with the pore at two different interfaces. When these changes are observed in fewer than four voltage sensors, the pore remains open, but when they are observed in all four voltage sensors, the pore constricts. The constriction occurs because the S4 helix, as it displaces inward, squeezes the right-handed helical bundle of pore-lining S6 helices. A similar conformational change occurs upon hyperpolarization of the EAG1 channel but with two helical turns displaced instead of one. Therefore, while K2.1 and EAG1 are from distinct architectural classes of voltage-dependent ion channels, called domain-swapped and non-domain-swapped, the way the voltage sensors gate their pores is very similar.
History
DepositionApr 3, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 28, 2025Provider: repository / Type: Initial release

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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


Theoretical massNumber of molelcules
Total (without water)384,0074
Polymers384,0074
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
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 / h-DRK1 / Voltage-gated potassium channel subunit Kv2.1


Mass: 96001.711 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KCNB1 / Production host: Homo sapiens (human) / References: UniProt: Q14721
Has protein modificationN

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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: human Kv2.1 / Type: CELL / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 13810 / Symmetry type: POINT
RefinementHighest resolution: 4.3 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0038548
ELECTRON MICROSCOPYf_angle_d0.44711572
ELECTRON MICROSCOPYf_dihedral_angle_d10.0763140
ELECTRON MICROSCOPYf_chiral_restr0.0361364
ELECTRON MICROSCOPYf_plane_restr0.0031408

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