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- EMDB-6689: Structure of a Pancreatic ATP-sensitive Potassium Channel -

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Basic information

Entry
Database: EMDB / ID: EMD-6689
TitleStructure of a Pancreatic ATP-sensitive Potassium Channel
Map data
SampleATP sensitive potassium
  • (ATP-sensitive inward rectifier potassium channel ...) x 2
  • (SUR1ABCC8) 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 / potassium ion import across plasma membrane / ankyrin binding ...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 / potassium ion import across plasma membrane / ankyrin binding / nervous system process / response to ATP / axolemma / intercalated disc / response to testosterone / potassium ion transmembrane transport / potassium ion binding / voltage-gated potassium channel activity / regulation of ion transmembrane transport / negative regulation of insulin secretion / regulation of insulin secretion / T-tubule / acrosomal vesicle / heat shock protein binding / response to ischemia / potassium ion transport / regulation of membrane potential / 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 / response to drug / intracellular membrane-bounded organelle / neuronal cell body / endoplasmic reticulum / mitochondrion / integral component of membrane / ATP binding / plasma membrane / cytosol
AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Potassium channel, inwardly rectifying, Kir, cytoplasmic / Potassium channel, inwardly rectifying, Kir / ABC transporter type 1, transmembrane domain / Sulphonylurea receptor / ABC transporter, conserved site / Immunoglobulin E-set / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like ...AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Potassium channel, inwardly rectifying, Kir, cytoplasmic / Potassium channel, inwardly rectifying, Kir / ABC transporter type 1, transmembrane domain / Sulphonylurea receptor / ABC transporter, conserved site / Immunoglobulin E-set / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like / Potassium channel, inwardly rectifying, transmembrane domain / Potassium channel, inwardly rectifying, Kir6.2 / Inward rectifier potassium channel, C-terminal / ATP-binding cassette subfamily C member 8
SUR1 / ATP-sensitive inward rectifier potassium channel 11
Biological speciesMus musculus (house mouse) / synthetic construct (others) / Mesocricetus auratus (golden hamster)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.6 Å
AuthorsLi N / Wu J-X / Chen L / Gao N
CitationJournal: Cell / Year: 2017
Title: Structure of a Pancreatic ATP-Sensitive Potassium Channel.
Authors: Ningning Li / Jing-Xiang Wu / Dian Ding / Jiaxuan Cheng / Ning Gao / Lei Chen /
Abstract: ATP-sensitive potassium channels (K) couple intracellular ATP levels with membrane excitability. These channels play crucial roles in many essential physiological processes and have been implicated ...ATP-sensitive potassium channels (K) couple intracellular ATP levels with membrane excitability. These channels play crucial roles in many essential physiological processes and have been implicated extensively in a spectrum of metabolic diseases and disorders. To gain insight into the mechanism of K, we elucidated the structure of a hetero-octameric pancreatic K channel in complex with a non-competitive inhibitor glibenclamide by single-particle cryoelectron microscopy to 5.6-Å resolution. The structure shows that four SUR1 regulatory subunits locate peripherally and dock onto the central Kir6.2 channel tetramer through the SUR1 TMD0-L0 fragment. Glibenclamide-bound SUR1 uses TMD0-L0 fragment to stabilize Kir6.2 channel in a closed conformation. In another structural population, a putative co-purified phosphatidylinositol 4,5-bisphosphate (PIP) molecule uncouples Kir6.2 from glibenclamide-bound SUR1. These structural observations suggest a molecular mechanism for K regulation by anti-diabetic sulfonylurea drugs, intracellular adenosine nucleotide concentrations, and PIP lipid.
Validation ReportPDB-ID: 5wua

SummaryFull reportAbout validation report
History
DepositionDec 16, 2016-
Header (metadata) releaseJan 25, 2017-
Map releaseJan 25, 2017-
UpdateJan 25, 2017-
Current statusJan 25, 2017Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.09
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.09
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5wua
  • Surface level: 0.09
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_6689.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 300 pix.
= 324. Å
1.08 Å/pix.
x 300 pix.
= 324. Å
1.08 Å/pix.
x 300 pix.
= 324. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density
Contour LevelBy AUTHOR: 0.09 / Movie #1: 0.09
Minimum - Maximum-0.2745838 - 0.39600915
Average (Standard dev.)0.0019237909 (±0.015809448)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 324.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.081.081.08
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z324.000324.000324.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.2750.3960.002

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Supplemental data

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Half map: #1

Fileemd_6689_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: #2

Fileemd_6689_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire ATP sensitive potassium

EntireName: ATP sensitive potassium / Number of components: 5

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Component #1: protein, ATP sensitive potassium

ProteinName: ATP sensitive potassium / Recombinant expression: No
MassTheoretical: 880 MDa
SourceSpecies: Mus musculus (house mouse)
Source (engineered)Expression System: Homo sapiens (human) / Vector: BacMam / Cell of expression system: HEK

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

ProteinName: ATP-sensitive inward rectifier potassium channel 11 / Recombinant expression: No

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Component #3: protein, SUR1

ProteinName: SUR1ABCC8 / Recombinant expression: No

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Component #4: protein, ATP-sensitive inward rectifier potassium channel 11,supe...

ProteinName: ATP-sensitive inward rectifier potassium channel 11,superfolder GFP
Details: ATP-sensitive inward rectifier potassium channel 11 with C-terminal synthetic superfolder GFP and affinity tags added
Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 76.339242 kDa
SourceSpecies: synthetic construct (others)
Source (engineered)Expression System: Homo sapiens (human)

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Component #5: protein, SUR1

ProteinName: SUR1ABCC8 / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 177.296578 kDa
SourceSpecies: Mesocricetus auratus (golden hamster)
Source (engineered)Expression System: Homo sapiens (human)

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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: 40 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C4 (4 fold cyclic) / Number of projections: 34500
3D reconstructionSoftware: relion / Resolution: 5.6 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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