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- EMDB-9789: Structure of a SUR1 fusion protein -

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Basic information

Entry
Database: EMDB / ID: EMD-9789
TitleStructure of a SUR1 fusion protein
Map data
Sample
  • Complex: KATPATP-sensitive potassium channel
Function / homology
Function and homology information


glutamate secretion, neurotransmission / inward rectifying potassium channel / sulfonylurea receptor activity / ATPase-coupled monoatomic cation transmembrane transporter activity / inorganic cation transmembrane transport / neuromuscular process / positive regulation of insulin secretion involved in cellular response to glucose stimulus / potassium channel activity / negative regulation of insulin secretion / ABC-type transporter activity ...glutamate secretion, neurotransmission / inward rectifying potassium channel / sulfonylurea receptor activity / ATPase-coupled monoatomic cation transmembrane transporter activity / inorganic cation transmembrane transport / neuromuscular process / positive regulation of insulin secretion involved in cellular response to glucose stimulus / potassium channel activity / negative regulation of insulin secretion / ABC-type transporter activity / ADP binding / presynapse / transmembrane transporter binding / ATP hydrolysis activity / ATP binding
Similarity search - Function
ATP-binding cassette subfamily C member 8 / Sulphonylurea receptor / 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 subfamily C member 8 / Sulphonylurea receptor / 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. / 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 isoform X2
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.45 Å
AuthorsChen L / Ding D / Wang M / Wu J-X / Kang Y
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.
History
DepositionJan 25, 2019-
Header (metadata) releaseMay 22, 2019-
Map releaseMay 22, 2019-
UpdateMay 22, 2019-
Current statusMay 22, 2019Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9789.png

Downloads & links

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Map

FileDownload / File: emd_9789.map.gz / Format: CCP4 / Size: 12.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.636 Å
Density
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.06
Minimum - Maximum-0.121678144 - 0.24714947
Average (Standard dev.)0.00090335426 (±0.00840658)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions150150150
Spacing150150150
CellA=B=C: 245.40001 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.6361.6361.636
M x/y/z150150150
origin x/y/z0.0000.0000.000
length x/y/z245.400245.400245.400
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ513513513
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS150150150
D min/max/mean-0.1220.2470.001

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Supplemental data

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Sample components

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Entire : KATP

EntireName: KATPATP-sensitive potassium channel
Components
  • Complex: KATPATP-sensitive potassium channel

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Supramolecule #1: KATP

SupramoleculeName: KATP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

6689

Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.45 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 118079
FSC plot (resolution estimation)

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