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- EMDB-35195: Rat Kir4.1 in complex with PIP2 -

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Basic information

Entry
Database: EMDB / ID: EMD-35195
TitleRat Kir4.1 in complex with PIP2
Map data
Sample
  • Complex: Rat Kir4.1 in complex with PIP2
    • Protein or peptide: ATP-sensitive inward rectifier potassium channel 10
  • Ligand: [(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
Keywordskir4.1 / ion channel / transport protein / MEMBRANE 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
ATP-sensitive inward rectifier potassium channel 10
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.85 Å
AuthorsZhao C / Guo J
Funding support China, 1 items
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, 2023-
Header (metadata) releaseFeb 28, 2024-
Map releaseFeb 28, 2024-
UpdateFeb 28, 2024-
Current statusFeb 28, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35195.png

Downloads & links

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Map

FileDownload / File: emd_35195.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.014 Å
Density
Contour LevelBy AUTHOR: 0.0137
Minimum - Maximum-0.027175736 - 0.069874756
Average (Standard dev.)-0.0000069376683 (±0.0034323353)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 182.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_35195_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_35195_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Rat Kir4.1 in complex with PIP2

EntireName: Rat Kir4.1 in complex with PIP2
Components
  • Complex: Rat Kir4.1 in complex with PIP2
    • Protein or peptide: ATP-sensitive inward rectifier potassium channel 10
  • Ligand: [(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

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Supramolecule #1: Rat Kir4.1 in complex with PIP2

SupramoleculeName: Rat Kir4.1 in complex with PIP2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Rattus norvegicus (Norway rat)

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Macromolecule #1: ATP-sensitive inward rectifier potassium channel 10

MacromoleculeName: ATP-sensitive inward rectifier potassium channel 10 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 38.791723 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GAPGIRRRRV LTKDGRSNVR MEHIADKRFL YLKDLWTTFI DMQWRYKLLL FSATFAGTWF LFGVVWYLVA VAHGDLLELG PPANHTPCV VQVHTLTGAF LFSLESQTTI GYGFRYISEE CPLAIVLLIA QLVLTTILEI FITGTFLAKI ARPKKRAETI R FSQHAVVA ...String:
GAPGIRRRRV LTKDGRSNVR MEHIADKRFL YLKDLWTTFI DMQWRYKLLL FSATFAGTWF LFGVVWYLVA VAHGDLLELG PPANHTPCV VQVHTLTGAF LFSLESQTTI GYGFRYISEE CPLAIVLLIA QLVLTTILEI FITGTFLAKI ARPKKRAETI R FSQHAVVA YHNGKLCLMI RVANMRKSLL IGCQVTGKLL QTHQTKEGEN IRLNQVNVTF QVDTASDSPF LILPLTFYHV VD ETSPLKD LPLRSGEGDF ELVLILSGTV ESTSATCQVR TSYLPEEILW GYEFTPAISL SASGKYVADF SLFDQVVKVA SPG GLRDST VRYGDPEKLK LDYKDDDDK

UniProtKB: ATP-sensitive inward rectifier potassium channel 10

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Macromolecule #2: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(o...

MacromoleculeName: [(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
type: ligand / ID: 2 / Number of copies: 4 / Formula: PIO
Molecular weightTheoretical: 746.566 Da
Chemical component information

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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Nominal defocus max: 1.4000000000000001 µm / Nominal defocus min: 1.2 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 62.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6xit

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 22786

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