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- EMDB-26320: Cryo-EM structure of the pancreatic ATP-sensitive potassium chann... -

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Basic information

Entry
Database: EMDB / ID: EMD-26320
TitleCryo-EM structure of the pancreatic ATP-sensitive potassium channel in the apo form with Kir6.2-CTD in the down conformation
Map data
Sample
  • Complex: KATP-ATP-CTDup
    • Complex: Kir6.2
    • Complex: SUR1
KeywordsKATP channel / SUR1 / Kir6.2 / ATP / sulfonylurea receptor / potassium transport / metabolic sensor / trafficking defects / MEMBRANE PROTEIN
Function / homology
Function and homology information


Regulation of insulin secretion / ATP sensitive Potassium channels / ABC-family proteins mediated transport / response to resveratrol / ATP-activated inward rectifier potassium channel activity / inward rectifying potassium channel / sulfonylurea receptor activity / cell body fiber / ventricular cardiac muscle tissue development / CAMKK-AMPK signaling cascade ...Regulation of insulin secretion / ATP sensitive Potassium channels / ABC-family proteins mediated transport / response to resveratrol / ATP-activated inward rectifier potassium channel activity / inward rectifying potassium channel / sulfonylurea receptor activity / cell body fiber / ventricular cardiac muscle tissue development / CAMKK-AMPK signaling cascade / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / ATPase-coupled monoatomic cation transmembrane transporter activity / inward rectifier potassium channel activity / regulation of monoatomic ion transmembrane transport / nervous system process / inorganic cation transmembrane transport / response to stress / ankyrin binding / Ion homeostasis / response to ATP / action potential / potassium ion import across plasma membrane / response to testosterone / voltage-gated potassium channel activity / intercalated disc / potassium channel activity / axolemma / ABC-type transporter activity / negative regulation of insulin secretion / cellular response to nutrient levels / heat shock protein binding / T-tubule / potassium ion transmembrane transport / regulation of insulin secretion / acrosomal vesicle / regulation of membrane potential / determination of adult lifespan / response to ischemia / positive regulation of protein localization to plasma membrane / cellular response to glucose stimulus / potassium ion transport / sarcolemma / cellular response to nicotine / glucose metabolic process / cellular response to tumor necrosis factor / nuclear envelope / response to estradiol / presynaptic membrane / transmembrane transporter binding / response to hypoxia / endosome / response to xenobiotic stimulus / neuronal cell body / glutamatergic synapse / apoptotic process / ATP hydrolysis activity / protein-containing complex / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
Potassium channel, inwardly rectifying, Kir6.2 / ATP-binding cassette subfamily C member 8 / Sulphonylurea receptor / Potassium channel, inwardly rectifying, transmembrane domain / Inward rectifier potassium channel transmembrane domain / Potassium channel, inwardly rectifying, Kir, cytoplasmic / Potassium channel, inwardly rectifying, Kir / Inward rectifier potassium channel, C-terminal / Inward rectifier potassium channel C-terminal domain / : ...Potassium channel, inwardly rectifying, Kir6.2 / ATP-binding cassette subfamily C member 8 / Sulphonylurea receptor / Potassium channel, inwardly rectifying, transmembrane domain / Inward rectifier potassium channel transmembrane domain / Potassium channel, inwardly rectifying, Kir, cytoplasmic / Potassium channel, inwardly rectifying, Kir / Inward rectifier potassium channel, C-terminal / Inward rectifier potassium channel C-terminal domain / : / 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. / Immunoglobulin E-set / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ATP-sensitive inward rectifier potassium channel 11 / ATP-binding cassette sub-family C member 8
Similarity search - Component
Biological speciesCricetus cricetus (black-bellied hamster) / Rattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM
AuthorsShyng SL / Sung MW / Driggers CM
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01 DK066485-13 United States
CitationJournal: Elife / Year: 2019
Title: Mechanism of pharmacochaperoning in a mammalian K channel revealed by cryo-EM.
Authors: Gregory M Martin / Min Woo Sung / Zhongying Yang / Laura M Innes / Balamurugan Kandasamy / Larry L David / Craig Yoshioka / Show-Ling Shyng /
Abstract: ATP-sensitive potassium (K) channels composed of a pore-forming Kir6.2 potassium channel and a regulatory ABC transporter sulfonylurea receptor 1 (SUR1) regulate insulin secretion in pancreatic β- ...ATP-sensitive potassium (K) channels composed of a pore-forming Kir6.2 potassium channel and a regulatory ABC transporter sulfonylurea receptor 1 (SUR1) regulate insulin secretion in pancreatic β-cells to maintain glucose homeostasis. Mutations that impair channel folding or assembly prevent cell surface expression and cause congenital hyperinsulinism. Structurally diverse K inhibitors are known to act as pharmacochaperones to correct mutant channel expression, but the mechanism is unknown. Here, we compare cryoEM structures of a mammalian K channel bound to pharmacochaperones glibenclamide, repaglinide, and carbamazepine. We found all three drugs bind within a common pocket in SUR1. Further, we found the N-terminus of Kir6.2 inserted within the central cavity of the SUR1 ABC core, adjacent the drug binding pocket. The findings reveal a common mechanism by which diverse compounds stabilize the Kir6.2 N-terminus within SUR1's ABC core, allowing it to act as a firm 'handle' for the assembly of metastable mutant SUR1-Kir6.2 complexes.
History
DepositionFeb 24, 2022-
Header (metadata) releaseAug 31, 2022-
Map releaseAug 31, 2022-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26320.png

Downloads & links

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Map

FileDownload / File: emd_26320.map.gz / Format: CCP4 / Size: 2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.83 Å/pix.
x 97 pix.
= 177.122 Å		1.83 Å/pix.
x 63 pix.
= 115.038 Å		1.83 Å/pix.
x 86 pix.
= 157.036 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.826 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0
Minimum - Maximum-10.027445 - 12.155486
Average (Standard dev.)0.000000000001979 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin624727
Dimensions638697
Spacing976386
CellA: 177.122 Å / B: 115.038 Å / C: 157.036 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : KATP-ATP-CTDup

EntireName: KATP-ATP-CTDup
Components
  • Complex: KATP-ATP-CTDup
    • Complex: Kir6.2
    • Complex: SUR1

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Supramolecule #1: KATP-ATP-CTDup

SupramoleculeName: KATP-ATP-CTDup / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Cricetus cricetus (black-bellied hamster)

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Supramolecule #2: Kir6.2

SupramoleculeName: Kir6.2 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 / Details: Adenovirus-based infection of INS-1 cells
Source (natural)Organism: Cricetus cricetus (black-bellied hamster)

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Supramolecule #3: SUR1

SupramoleculeName: SUR1 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 / Details: Adenovirus-based infection of INS-1 cells
Source (natural)Organism: Rattus norvegicus (Norway rat)

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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
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

7073

Initial angle assignmentType: COMMON LINE
Final angle assignmentType: ANGULAR RECONSTITUTION

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Atomic model buiding 1

Initial model
PDB IDChain

6baa

chain_id: A, source_name: PDB, initial_model_type: experimental model

6baa

chain_id: B, source_name: PDB, initial_model_type: experimental model

6baa

chain_id: C, source_name: PDB, initial_model_type: experimental model

6baa

chain_id: D, source_name: PDB, initial_model_type: experimental model

6pz9

chain_id: E, source_name: PDB, initial_model_type: experimental model
Output model

PDB-7uqr:
Cryo-EM structure of the pancreatic ATP-sensitive potassium channel in the apo form with Kir6.2-CTD in the down conformation

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