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- EMDB-9788: Structure of SUR1 subunit bound with repaglinide -

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Basic information

Entry
Database: EMDB / ID: EMD-9788
TitleStructure of SUR1 subunit bound with repaglinide
Map data
SampleSUR1ABCC8
  • ATP-binding cassette sub-family C member 8 isoform X2
  • (ligand) x 2
Function / homology
Function and homology information


sulfonylurea receptor activity / inorganic cation transmembrane transport / ATPase-coupled cation transmembrane transporter activity / potassium ion transport / ATPase activity / integral component of membrane / ATP binding / plasma membrane
Sulphonylurea receptor / P-loop containing nucleoside triphosphate hydrolase / ABC transporter type 1, transmembrane domain superfamily / ATP-binding cassette subfamily C member 8 / ABC transporter-like / AAA+ ATPase domain / ABC transporter type 1, transmembrane domain / ABC transporter, conserved site
ATP-binding cassette sub-family C member 8 isoform X2
Biological speciesMus musculus (house mouse) / Mesocricetus auratus (golden hamster)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.53 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: 6jb3

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: 0.08
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.08
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6jb3
  • Surface level: 0.08
  • 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_9788.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: 0.08 / Movie #1: 0.08
Minimum - Maximum-0.18529668 - 0.34005585
Average (Standard dev.)0.00027882177 (±0.005020385)
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-0.1850.3400.000

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Supplemental data

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Additional map: #1

Fileemd_9788_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: sharpened map with a bfactor -100

Fileemd_9788_additional_2.map
Annotationsharpened map with a bfactor -100
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire SUR1

EntireName: SUR1ABCC8 / Number of components: 4

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Component #1: protein, SUR1

ProteinName: SUR1ABCC8 / Recombinant expression: No
SourceSpecies: Mus musculus (house mouse)
Source (engineered)Expression System: Homo sapiens (human)

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Component #2: 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: 1 / Recombinant expression: No
MassTheoretical: 177.295516 kDa
SourceSpecies: Mesocricetus auratus (golden hamster)
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: ligand, Repaglinide

LigandName: Repaglinide / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.452586 kDa

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Component #4: ligand, Digitonin

LigandName: Digitonin / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 1.229312 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: 653991
3D reconstructionSoftware: RELION / Resolution: 3.53 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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