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- PDB-8i5n: Rat Kir4.1 in complex with PIP2 and Lys05 -

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Basic information

Entry
Database: PDB / ID: 8i5n
TitleRat Kir4.1 in complex with PIP2 and Lys05
ComponentsATP-sensitive inward rectifier potassium channel 10
KeywordsMEMBRANE PROTEIN / kir4.1 / ion channel / transport protein
Function / homology
Function and homology information


glutamate reuptake / Potassium transport channels / L-glutamate import / response to blue light / central nervous system myelination / response to mineralocorticoid / regulation of resting membrane potential / cellular response to potassium ion / oligodendrocyte development / astrocyte projection ...glutamate reuptake / Potassium transport channels / L-glutamate import / response to blue light / central nervous system myelination / response to mineralocorticoid / regulation of resting membrane potential / cellular response to potassium ion / oligodendrocyte development / astrocyte projection / inward rectifier potassium channel activity / potassium ion homeostasis / membrane hyperpolarization / non-motile cilium assembly / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / optic nerve development / regulation of monoatomic ion transmembrane transport / adult walking behavior / ciliary base / monoatomic ion channel complex / potassium ion import across plasma membrane / microvillus / potassium channel activity / response to glucocorticoid / potassium ion transmembrane transport / visual perception / regulation of membrane potential / establishment of localization in cell / regulation of long-term neuronal synaptic plasticity / potassium ion transport / presynapse / cell body / basolateral plasma membrane / apical plasma membrane / signaling receptor binding / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
Potassium channel, inwardly rectifying, Kir1.2 / Potassium channel, inwardly rectifying, transmembrane domain / Inward rectifier potassium channel transmembrane domain / Potassium channel, inwardly rectifying, Kir, cytoplasmic / Potassium channel, inwardly rectifying, Kir / Inward rectifier potassium channel, C-terminal / Inward rectifier potassium channel C-terminal domain / Immunoglobulin E-set
Similarity search - Domain/homology
Chem-PIO / ATP-sensitive inward rectifier potassium channel 10
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.85 Å
AuthorsZhao, C. / Guo, J.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Education (MoE, China)Frontier Science Center for Brain Science & Brain-Machine Integration, Zhejiang University China
CitationJournal: To Be Published
Title: Pharmacological inhibition of astrocytic Kir4.1 channel evokes rapid-onset antidepressant responses
Authors: Zhao, C. / Guo, J.
History
DepositionJan 26, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-sensitive inward rectifier potassium channel 10
B: ATP-sensitive inward rectifier potassium channel 10
C: ATP-sensitive inward rectifier potassium channel 10
D: ATP-sensitive inward rectifier potassium channel 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,1538
Polymers155,1674
Non-polymers2,9864
Water0
1


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

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Components

#1: Protein
ATP-sensitive inward rectifier potassium channel 10 / ATP-sensitive inward rectifier potassium channel KAB-2 / BIR10 / Brain-specific inwardly rectifying ...ATP-sensitive inward rectifier potassium channel KAB-2 / BIR10 / Brain-specific inwardly rectifying K(+) channel 1 / BIRK1 / Inward rectifier K(+) channel Kir4.1 / Potassium channel / inwardly rectifying subfamily J member 10


Mass: 38791.723 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Kcnj10, Kab-2 / Cell (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P49655
#2: Chemical
ChemComp-PIO / [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate / dioctanoyl l-alpha-phosphatidyl-d-myo-inositol 4,5-diphosphate


Mass: 746.566 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C25H49O19P3 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: Rat Kir4.1 in complex with PIP2 and Lys05 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Rattus norvegicus (Norway rat)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: DARK FIELD / Nominal defocus max: 1400 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 62 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 75833 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00920396
ELECTRON MICROSCOPYf_angle_d1.34636912
ELECTRON MICROSCOPYf_dihedral_angle_d12.5258148
ELECTRON MICROSCOPYf_chiral_restr0.0811652
ELECTRON MICROSCOPYf_plane_restr0.0042900

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