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- EMDB-9787: Structure of pancreatic ATP-sensitive potassium channel bound wit... -

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Basic information

Entry
Database: EMDB / ID: EMD-9787
TitleStructure of pancreatic ATP-sensitive potassium channel bound with repaglinide and ATPgammaS at 3.3A resolution
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 5
Function / homology
Function and homology information


ATP sensitive Potassium channels / ABC-family proteins mediated transport / Regulation of insulin secretion / Ion homeostasis / inward rectifying potassium channel / ATP-activated inward rectifier potassium channel activity / sulfonylurea receptor activity / cell body fiber / inward rectifier potassium channel activity / positive regulation of cation channel activity ...ATP sensitive Potassium channels / ABC-family proteins mediated transport / Regulation of insulin secretion / Ion homeostasis / inward rectifying potassium channel / ATP-activated inward rectifier potassium channel activity / sulfonylurea receptor activity / cell body fiber / inward rectifier potassium channel activity / positive regulation of cation channel activity / response to ATP / potassium ion import across plasma membrane / ankyrin binding / axolemma / nervous system process / intercalated disc / potassium ion transmembrane transport / potassium ion binding / response to testosterone / ATPase-coupled transmembrane transporter activity / voltage-gated potassium channel activity / T-tubule / negative regulation of insulin secretion / regulation of membrane potential / regulation of insulin secretion / response to ischemia / acrosomal vesicle / potassium ion transport / heat shock protein binding / 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 / ion channel binding / response to estradiol / response to drug / protein C-terminus binding / endosome / ATPase activity / intracellular membrane-bounded organelle / neuronal cell body / endoplasmic reticulum / mitochondrion / integral component of membrane / ATP binding / plasma membrane / cytosol
Inward rectifier potassium channel, C-terminal / P-loop containing nucleoside triphosphate hydrolase / ABC transporter, conserved site / ABC transporter type 1, transmembrane domain superfamily / Potassium channel, inwardly rectifying, transmembrane domain / Sulphonylurea receptor / ABC transporter-like / Potassium channel, inwardly rectifying, Kir / ATP-binding cassette subfamily C member 8 / Immunoglobulin E-set ...Inward rectifier potassium channel, C-terminal / P-loop containing nucleoside triphosphate hydrolase / ABC transporter, conserved site / ABC transporter type 1, transmembrane domain superfamily / Potassium channel, inwardly rectifying, transmembrane domain / Sulphonylurea receptor / ABC transporter-like / Potassium channel, inwardly rectifying, Kir / ATP-binding cassette subfamily C member 8 / Immunoglobulin E-set / ABC transporter / Potassium channel, inwardly rectifying, Kir, cytoplasmic / Potassium channel, inwardly rectifying, Kir6.2 / ABC transporter transmembrane region / Inward rectifier potassium channel transmembrane domain / Inward rectifier potassium channel C-terminal domain / ABC transporters family signature. / ATP-binding cassette, ABC transporter-type domain profile. / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain / AAA+ ATPase domain
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: 3.3 Å
AuthorsChen L / Ding D / Wang M / Wu J-X / Kang Y
Funding support China, 4 items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2016YFA0502004 China
National Natural Science Foundation of China31821091 China
National Natural Science Foundation of China31622021 China
National Natural Science Foundation of China31870833 China
CitationJournal: Cell Rep / Year: 2019
Title: The Structural Basis for the Binding of Repaglinide to the Pancreatic K Channel.
Authors: Dian Ding / Mengmeng Wang / Jing-Xiang Wu / Yunlu Kang / Lei Chen /
Abstract: Repaglinide (RPG) is a short-acting insulin secretagogue widely prescribed for the treatment of type 2 diabetes. It boosts insulin secretion by inhibiting the pancreatic ATP-sensitive potassium ...Repaglinide (RPG) is a short-acting insulin secretagogue widely prescribed for the treatment of type 2 diabetes. It boosts insulin secretion by inhibiting the pancreatic ATP-sensitive potassium channel (K). However, the mechanisms by which RPG binds to the K channel are poorly understood. Here, we describe two cryo-EM structures: the pancreatic K channel in complex with inhibitory RPG and adenosine-5'-(γ-thio)-triphosphate (ATPγS) at 3.3 Å and a medium-resolution structure of a RPG-bound mini SUR1 protein in which the N terminus of the inward-rectifying potassium channel 6.1 (Kir6.1) is fused to the ABC transporter module of the sulfonylurea receptor 1 (SUR1). These structures reveal the binding site of RPG in the SUR1 subunit. Furthermore, the high-resolution structure reveals the complex architecture of the ATP binding site, which is formed by both Kir6.2 and SUR1 subunits, and the domain-domain interaction interfaces.
Validation ReportPDB-ID: 6jb1

SummaryFull reportAbout validation report
History
DepositionJan 25, 2019-
Header (metadata) releaseMay 22, 2019-
Map releaseMay 22, 2019-
UpdateNov 6, 2019-
Current statusNov 6, 2019Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.8
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 3.8
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6jb1
  • Surface level: 3.8
  • 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_9787.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 256 pix.
= 338.944 Å
1.32 Å/pix.
x 256 pix.
= 338.944 Å
1.32 Å/pix.
x 256 pix.
= 338.944 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.324 Å
Density
Contour LevelBy AUTHOR: 3.8 / Movie #1: 3.8
Minimum - Maximum-15.475457 - 27.763676
Average (Standard dev.)0.09481621 (±0.833791)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 338.944 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3241.3241.324
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z338.944338.944338.944
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ513513513
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-15.47527.7640.095

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Supplemental data

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Sample components

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Entire KATP

EntireName: KATPATP-sensitive potassium channel / Number of components: 8

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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, (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propy...

LigandName: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
Number of Copies: 36 / Recombinant expression: No
MassTheoretical: 0.760076 kDa

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Component #5: 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 #6: ligand, Digitonin

LigandName: Digitonin / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 1.229312 kDa

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Component #7: ligand, Repaglinide

LigandName: Repaglinide / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 0.452586 kDa

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Component #8: ligand, PHOSPHATIDYLETHANOLAMINE

LigandName: PHOSPHATIDYLETHANOLAMINE / Number of Copies: 16 / Recombinant expression: No
MassTheoretical: 0.734039 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 / Applied symmetry: C4 (4 fold cyclic) / Number of projections: 277548
3D reconstructionSoftware: RELION / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

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