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- EMDB-6833: Structure of pancreatic ATP-sensitive potassium channel bound wit... -

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Basic information

Entry
Database: EMDB / ID: EMD-6833
TitleStructure of pancreatic ATP-sensitive potassium channel bound with glibenclamide and ATPgammaS (Class2 at 4.57A)
Map data
SampleKATPATP-sensitive potassium channel
  • ATP-sensitive inward rectifier potassium channel 11
  • ATP-binding cassette sub-family C member 8 isoform X2
  • (ligand) x 2
Function / homology
Function and homology information


inward rectifying potassium channel / ATP-activated inward rectifier potassium channel activity / sulfonylurea receptor activity / cell body fiber / inorganic cation transmembrane transport / ATPase-coupled cation transmembrane transporter activity / inward rectifier potassium channel activity / positive regulation of cation channel activity / ankyrin binding / nervous system process ...inward rectifying potassium channel / ATP-activated inward rectifier potassium channel activity / sulfonylurea receptor activity / cell body fiber / inorganic cation transmembrane transport / ATPase-coupled cation transmembrane transporter activity / inward rectifier potassium channel activity / positive regulation of cation channel activity / ankyrin binding / nervous system process / potassium ion import across plasma membrane / response to ATP / axolemma / intercalated disc / response to testosterone / potassium ion binding / potassium ion transmembrane transport / voltage-gated potassium channel activity / regulation of ion transmembrane transport / negative regulation of insulin secretion / regulation of insulin secretion / regulation of membrane potential / heat shock protein binding / T-tubule / acrosomal vesicle / response to ischemia / potassium ion transport / cellular response to glucose stimulus / sarcolemma / positive regulation of protein localization to plasma membrane / nuclear envelope / cellular response to nicotine / glucose metabolic process / cellular response to tumor necrosis factor / myelin sheath / response to estradiol / ion channel binding / protein C-terminus binding / endosome / ATPase activity / intracellular membrane-bounded organelle / neuronal cell body / response to drug / endoplasmic reticulum / mitochondrion / integral component of membrane / ATP binding / plasma membrane / cytosol
Potassium channel, inwardly rectifying, Kir, cytoplasmic / Potassium channel, inwardly rectifying, Kir / ABC transporter type 1, transmembrane domain / Inward rectifier potassium channel, C-terminal / AAA+ ATPase domain / Potassium channel, inwardly rectifying, transmembrane domain / ABC transporter-like / ABC transporter type 1, transmembrane domain superfamily / P-loop containing nucleoside triphosphate hydrolase / ABC transporter, conserved site ...Potassium channel, inwardly rectifying, Kir, cytoplasmic / Potassium channel, inwardly rectifying, Kir / ABC transporter type 1, transmembrane domain / Inward rectifier potassium channel, C-terminal / AAA+ ATPase domain / Potassium channel, inwardly rectifying, transmembrane domain / ABC transporter-like / ABC transporter type 1, transmembrane domain superfamily / P-loop containing nucleoside triphosphate hydrolase / ABC transporter, conserved site / Potassium channel, inwardly rectifying, Kir6.2 / ATP-binding cassette subfamily C member 8 / Sulphonylurea receptor / Immunoglobulin E-set
ATP-binding cassette sub-family C member 8 isoform X2 / ATP-sensitive inward rectifier potassium channel 11
Biological speciesMus musculus (house mouse) / Mesocricetus auratus (golden hamster)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.57 Å
AuthorsChen L / Wu JX
CitationJournal: Protein Cell / Year: 2018
Title: Ligand binding and conformational changes of SUR1 subunit in pancreatic ATP-sensitive potassium channels.
Authors: Jing-Xiang Wu / Dian Ding / Mengmeng Wang / Yunlu Kang / Xin Zeng / Lei Chen /
Abstract: ATP-sensitive potassium channels (K) are energy sensors on the plasma membrane. By sensing the intracellular ADP/ATP ratio of β-cells, pancreatic K channels control insulin release and regulate ...ATP-sensitive potassium channels (K) are energy sensors on the plasma membrane. By sensing the intracellular ADP/ATP ratio of β-cells, pancreatic K channels control insulin release and regulate metabolism at the whole body level. They are implicated in many metabolic disorders and diseases and are therefore important drug targets. Here, we present three structures of pancreatic K channels solved by cryo-electron microscopy (cryo-EM), at resolutions ranging from 4.1 to 4.5 Å. These structures depict the binding site of the antidiabetic drug glibenclamide, indicate how Kir6.2 (inward-rectifying potassium channel 6.2) N-terminus participates in the coupling between the peripheral SUR1 (sulfonylurea receptor 1) subunit and the central Kir6.2 channel, reveal the binding mode of activating nucleotides, and suggest the mechanism of how Mg-ADP binding on nucleotide binding domains (NBDs) drives a conformational change of the SUR1 subunit.
Validation ReportPDB-ID: 5ykg

SummaryFull reportAbout validation report
History
DepositionOct 14, 2017-
Header (metadata) releaseApr 18, 2018-
Map releaseApr 18, 2018-
UpdateJun 13, 2018-
Current statusJun 13, 2018Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.022
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.022
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5ykg
  • Surface level: 0.022
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_6833.map.gz / Format: CCP4 / Size: 115.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 312 pix.
= 329.16 Å
1.06 Å/pix.
x 312 pix.
= 329.16 Å
1.06 Å/pix.
x 312 pix.
= 329.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.055 Å
Density
Contour LevelBy AUTHOR: 0.022 / Movie #1: 0.022
Minimum - Maximum-0.034367453 - 0.082241215
Average (Standard dev.)0.0011559395 (±0.0049148095)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions312312312
Spacing312312312
CellA=B=C: 329.15997 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0551.0551.055
M x/y/z312312312
origin x/y/z0.0000.0000.000
length x/y/z329.160329.160329.160
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS312312312
D min/max/mean-0.0340.0820.001

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Supplemental data

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Half map: #1

Fileemd_6833_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: #2

Fileemd_6833_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Sample components

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Entire KATP

EntireName: KATPATP-sensitive potassium channel / Number of components: 5

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Component #1: protein, KATP

ProteinName: KATPATP-sensitive potassium channel / Recombinant expression: No
SourceSpecies: Mus musculus (house mouse)
Source (engineered)Expression System: Homo sapiens (human)

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Component #2: protein, ATP-sensitive inward rectifier potassium channel 11

ProteinName: ATP-sensitive inward rectifier potassium channel 11 / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 43.615734 kDa
SourceSpecies: Mus musculus (house mouse)
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: protein, ATP-binding cassette sub-family C member 8 isoform X2

ProteinName: ATP-binding cassette sub-family C member 8 isoform X2 / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 177.295516 kDa
SourceSpecies: Mesocricetus auratus (golden hamster)
Source (engineered)Expression System: Homo sapiens (human)

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Component #4: ligand, PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

LigandName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Number of Copies: 8 / Recombinant expression: No
MassTheoretical: 0.523247 kDa

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Component #5: ligand, 5-chloro-N-(2-{4-[(cyclohexylcarbamoyl)sulfamoyl]phenyl}e...

LigandName: 5-chloro-N-(2-{4-[(cyclohexylcarbamoyl)sulfamoyl]phenyl}ethyl)-2-methoxybenzamide
Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 0.494004 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 50 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 40340
3D reconstructionSoftware: RELION / Resolution: 4.57 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Output model

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