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- EMDB-3265: Single particle analysis of ATP-sensitive potassium channel -

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Basic information

Entry
Database: EMDB / ID: EMD-3265
TitleSingle particle analysis of ATP-sensitive potassium channel
Map dataHeterooctamer complex of hamster SUR1 and mouse Kir6.2
Sample
  • Sample: ATP-sensitive potassium channel complex consisting of hamster SUR1 and mouse Kir6.2
  • Protein or peptide: ATP-binding cassette sub-family C member 8
  • Protein or peptide: ATP-sensitive inward rectifier potassium channel 11
Keywordspotassium channel / ABC transporter / ATP-sensitive potassium channel
Function / homology
Function and homology information


ATP sensitive Potassium channels / response to resveratrol / ATP-activated inward rectifier potassium channel activity / inward rectifying potassium channel / Regulation of insulin secretion / sulfonylurea receptor activity / ventricular cardiac muscle tissue development / cell body fiber / ABC-family proteins mediated transport / CAMKK-AMPK signaling cascade ...ATP sensitive Potassium channels / response to resveratrol / ATP-activated inward rectifier potassium channel activity / inward rectifying potassium channel / Regulation of insulin secretion / sulfonylurea receptor activity / ventricular cardiac muscle tissue development / cell body fiber / ABC-family proteins mediated transport / CAMKK-AMPK signaling cascade / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / inward rectifier potassium channel activity / ATPase-coupled monoatomic cation transmembrane transporter activity / Ion homeostasis / nervous system process / ankyrin binding / response to ATP / response to stress / potassium ion import across plasma membrane / potassium ion binding / response to testosterone / action potential / axolemma / intercalated disc / potassium channel activity / ABC-type transporter activity / cellular response to nutrient levels / negative regulation of insulin secretion / heat shock protein binding / T-tubule / acrosomal vesicle / response to ischemia / determination of adult lifespan / positive regulation of protein localization to plasma membrane / cellular response to glucose stimulus / cellular response to nicotine / glucose metabolic process / nuclear envelope / cellular response to tumor necrosis factor / response to estradiol / presynaptic membrane / transmembrane transporter binding / response to hypoxia / endosome / response to xenobiotic stimulus / neuronal cell body / apoptotic process / glutamatergic synapse / protein-containing complex / ATP hydrolysis activity / ATP binding / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Potassium channel, inwardly rectifying, Kir6.2 / ATP-binding cassette subfamily C member 8 / Sulphonylurea receptor / 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 / : ...Potassium channel, inwardly rectifying, Kir6.2 / ATP-binding cassette subfamily C member 8 / Sulphonylurea receptor / 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 / : / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / Immunoglobulin E-set / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ATP-binding cassette sub-family C member 8 / ATP-sensitive inward rectifier potassium channel 11
Similarity search - Component
Biological speciesCricetus cricetus (black-bellied hamster) / Mus musculus (house mouse)
Methodsingle particle reconstruction / negative staining / Resolution: 18.0 Å
AuthorsKimura Y / Kanno R / Matsuo M / Kato H / Mitsuoka K / Kazumitsu U
CitationJournal: The Journal of Biological Chemistry
Title: Nucleotide-dependent conformational change of the ATP-sensitive potassium channel
Authors: Kimura Y / Kanno R / Matsuo M / Kato H / Mitsuoka K / Kazumitsu U
History
DepositionNov 27, 2015-
Header (metadata) releaseJan 27, 2016-
Map releaseMay 31, 2017-
UpdateMay 31, 2017-
Current statusMay 31, 2017Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.23
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.23
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3265.png

Downloads & links

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Map

FileDownload / File: emd_3265.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHeterooctamer complex of hamster SUR1 and mouse Kir6.2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.6 Å/pix.
x 100 pix.
= 360. Å		3.6 Å/pix.
x 100 pix.
= 360. Å		3.6 Å/pix.
x 100 pix.
= 360. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.6 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.23 / Movie #1: 0.23
Minimum - Maximum-0.31650114 - 0.79723728
Average (Standard dev.)0.01637996 (±0.08898084)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-49-50-50
Dimensions100100100
Spacing100100100
CellA=B=C: 360.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.63.63.6
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z360.000360.000360.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-50-49-50
NC/NR/NS100100100
D min/max/mean-0.3170.7970.016

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Supplemental data

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Sample components

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Entire : ATP-sensitive potassium channel complex consisting of hamster SUR...

EntireName: ATP-sensitive potassium channel complex consisting of hamster SUR1 and mouse Kir6.2
Components
  • Sample: ATP-sensitive potassium channel complex consisting of hamster SUR1 and mouse Kir6.2
  • Protein or peptide: ATP-binding cassette sub-family C member 8
  • Protein or peptide: ATP-sensitive inward rectifier potassium channel 11

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Supramolecule #1000: ATP-sensitive potassium channel complex consisting of hamster SUR...

SupramoleculeName: ATP-sensitive potassium channel complex consisting of hamster SUR1 and mouse Kir6.2
type: sample / ID: 1000
Oligomeric state: Four SUR1 and four Kir6.2 forms heterooctamer
Number unique components: 2
Molecular weightTheoretical: 880 KDa

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Macromolecule #1: ATP-binding cassette sub-family C member 8

MacromoleculeName: ATP-binding cassette sub-family C member 8 / type: protein_or_peptide / ID: 1 / Name.synonym: ABCC8, SUR1 / Number of copies: 4 / Recombinant expression: Yes
Source (natural)Organism: Cricetus cricetus (black-bellied hamster) / synonym: Black-bellied hamster
Molecular weightTheoretical: 180 KDa
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant strain: human / Recombinant cell: FreeStyle 293F / Recombinant plasmid: pCDNA3.1
SequenceUniProtKB: ATP-binding cassette sub-family C member 8

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Macromolecule #2: ATP-sensitive inward rectifier potassium channel 11

MacromoleculeName: ATP-sensitive inward rectifier potassium channel 11 / type: protein_or_peptide / ID: 2 / Name.synonym: KCNJ11, Kir6.2 / Number of copies: 4 / Recombinant expression: Yes
Source (natural)Organism: Mus musculus (house mouse) / synonym: Mouse
Molecular weightTheoretical: 44 KDa
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant strain: human / Recombinant cell: FreeStyle 293F / Recombinant plasmid: pCDNA3.1
SequenceUniProtKB: ATP-sensitive inward rectifier potassium channel 11

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.1 mg/mL
BufferpH: 7.2
Details: 50 mM HEPES-Na, 50 mM NaCl, 50 mM KCl, 5% glycerol, 1 mM 2-mercaptoethanol, 0.05% C12E8
StainingType: NEGATIVE
Details: Purified protein was stained with 2% uranyl acetate for 10 seconds on a carbon-coated copper grid
GridDetails: 400 mesh copper grid with thin carbon support, glow discharged
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeJEOL 1010
DateJun 9, 2009
Image recordingCategory: CCD / Film or detector model: OTHER / Number real images: 34 / Bits/pixel: 8
Tilt angle min0
Tilt angle max0
Electron beamAcceleration voltage: 100 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsCalibrated magnification: 38400 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal magnification: 30000
Sample stageSpecimen holder model: JEOL

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Image processing

DetailsThe particles were selected using an automatic selection program.
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 18.0 Å / Resolution method: OTHER / Software - Name: IMAGIC / Number images used: 12117
Final two d classificationNumber classes: 82

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