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- PDB-8teo: Shaker in low K+ (4mM K+) -

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Basic information

Entry
Database: PDB / ID: 8teo
TitleShaker in low K+ (4mM K+)
ComponentsPotassium voltage-gated channel protein ShakerVoltage-gated potassium channel
KeywordsMEMBRANE PROTEIN / voltage-gated potassium channel
Function / homology
Function and homology information


mating behavior, sex discrimination / Phase 3 - rapid repolarisation / behavioral response to ether / Voltage gated Potassium channels / proboscis extension reflex / larval locomotory behavior / regulation of synaptic activity / courtship behavior / positive regulation of membrane potential / positive regulation of circadian sleep/wake cycle, sleep ...mating behavior, sex discrimination / Phase 3 - rapid repolarisation / behavioral response to ether / Voltage gated Potassium channels / proboscis extension reflex / larval locomotory behavior / regulation of synaptic activity / courtship behavior / positive regulation of membrane potential / positive regulation of circadian sleep/wake cycle, sleep / regulation of circadian sleep/wake cycle, sleep / detection of visible light / cellular response to dopamine / voltage-gated monoatomic cation channel activity / sleep / delayed rectifier potassium channel activity / axon extension / action potential / voltage-gated potassium channel activity / potassium ion transmembrane transport / voltage-gated potassium channel complex / protein homooligomerization / potassium ion transport / sensory perception of taste / learning or memory / membrane
Similarity search - Function
Potassium channel, voltage dependent, Kv1 / 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 protein Shaker
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.39 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: Sci Adv / Year: 2023
Title: Eukaryotic Kv channel Shaker inactivates through selectivity filter dilation rather than collapse.
Authors: Robyn Stix / Xiao-Feng Tan / Chanhyung Bae / Ana I Fernández-Mariño / Kenton J Swartz / José D Faraldo-Gómez /
Abstract: Eukaryotic voltage-gated K channels have been extensively studied, but the structural bases for some of their most salient functional features remain to be established. C-type inactivation, for ...Eukaryotic voltage-gated K channels have been extensively studied, but the structural bases for some of their most salient functional features remain to be established. C-type inactivation, for example, is an auto-inhibitory mechanism that confers temporal resolution to their signal-firing activity. In a recent breakthrough, studies of a mutant of Shaker that is prone to inactivate indicated that this process entails a dilation of the selectivity filter, the narrowest part of the ion conduction pathway. Here, we report an atomic-resolution cryo-electron microscopy structure that demonstrates that the wild-type channel can also adopt this dilated state. All-atom simulations corroborate this conformation is congruent with the electrophysiological characteristics of the C-type inactivated state, namely, residual K conductance and altered ion specificity, and help rationalize why inactivation is accelerated or impeded by certain mutations. In summary, this study establishes the molecular basis for an important self-regulatory mechanism in eukaryotic K channels, laying a solid foundation for further studies.
History
DepositionJul 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Potassium voltage-gated channel protein Shaker
B: Potassium voltage-gated channel protein Shaker
C: Potassium voltage-gated channel protein Shaker
D: Potassium voltage-gated channel protein Shaker
hetero molecules


Theoretical massNumber of molelcules
Total (without water)322,50438
Polymers298,1044
Non-polymers24,40134
Water1629
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Potassium voltage-gated channel protein Shaker / Voltage-gated potassium channel / Protein minisleep


Mass: 74525.953 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Sh, mns, CG12348 / Cell line (production host): HEK TSA201 / Production host: Homo sapiens (human) / References: UniProt: P08510
#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.: 32 / Source method: obtained synthetically / Formula: C42H82NO8P / Comment: phospholipid*YM
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O
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-gated potassium channel Shaker / Type: CELL / Entity ID: #1 / Source: NATURAL
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenConc.: 4.5 mg/ml / Embedding 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 % / Chamber temperature: 289 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / 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: 52 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.19.1_4122: / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 2.39 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 663447 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0036612
ELECTRON MICROSCOPYf_angle_d0.5428868
ELECTRON MICROSCOPYf_dihedral_angle_d13.3862380
ELECTRON MICROSCOPYf_chiral_restr0.0421072
ELECTRON MICROSCOPYf_plane_restr0.0081020

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