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- PDB-5ywa: Structure of pancreatic ATP-sensitive potassium channel bound wit... -

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Basic information

Entry
Database: PDB / ID: 5ywa
TitleStructure of pancreatic ATP-sensitive potassium channel bound with ATPgammaS (CTD class 2 at 6.1A)
Components
  • ATP-binding cassette sub-family C member 8 isoform X2
  • ATP-sensitive inward rectifier potassium channel 11
KeywordsMEMBRANE PROTEIN / KATP / channel / glibenclamide / sulfonylurea
Function / homology
Function and homology information


ATP sensitive Potassium channels / response to resveratrol / ATP-activated inward rectifier potassium channel activity / glutamate secretion, neurotransmission / inward rectifying potassium channel / Regulation of insulin secretion / sulfonylurea receptor activity / ventricular cardiac muscle tissue development / cell body fiber / ABC-family proteins mediated transport ...ATP sensitive Potassium channels / response to resveratrol / ATP-activated inward rectifier potassium channel activity / glutamate secretion, neurotransmission / inward rectifying potassium channel / Regulation of insulin secretion / sulfonylurea receptor activity / ventricular cardiac muscle tissue development / cell body fiber / ABC-family proteins mediated transport / CAMKK-AMPK signaling cascade / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / Ion homeostasis / inward rectifier potassium channel activity / ATPase-coupled monoatomic cation transmembrane transporter activity / nervous system process / inorganic cation transmembrane transport / ankyrin binding / neuromuscular process / response to ATP / response to stress / potassium ion import across plasma membrane / response to testosterone / potassium ion binding / positive regulation of insulin secretion involved in cellular response to glucose stimulus / potassium channel activity / action potential / intercalated disc / axolemma / ABC-type transporter activity / negative regulation of insulin secretion / cellular response to nutrient levels / heat shock protein binding / T-tubule / acrosomal vesicle / response to ischemia / determination of adult lifespan / positive regulation of protein localization to plasma membrane / cellular response to glucose stimulus / ADP binding / cellular response to nicotine / glucose metabolic process / nuclear envelope / cellular response to tumor necrosis factor / response to estradiol / presynapse / presynaptic membrane / transmembrane transporter binding / response to hypoxia / endosome / response to xenobiotic stimulus / neuronal cell body / apoptotic process / glutamatergic synapse / ATP hydrolysis activity / 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
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-binding cassette sub-family C member 8 isoform X2 / ATP-sensitive inward rectifier potassium channel 11
Similarity search - Component
Biological speciesMus musculus (house mouse)
Mesocricetus auratus (golden hamster)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.1 Å
AuthorsChen, L. / Wu, J.X.
Funding support China, 5items
OrganizationGrant numberCountry
Ministry of Science and Technology of China2016YFA0502004 China
National Natural Science Foundation of China31622021 China
National Natural Science Foundation of China31521062 China
China Postdoctoral Science Foundation2016M600856 China
China Postdoctoral Science Foundation2017T100014 China
CitationJournal: Protein Cell / Year: 2018
Title: Ligand binding and conformational changes of SUR1 subunit in pancreatic ATP-sensitive potassium channels.
Authors: Jing-Xiang Wu / Dian Ding / Mengmeng Wang / Yunlu Kang / Xin Zeng / Lei Chen /
Abstract: ATP-sensitive potassium channels (K) are energy sensors on the plasma membrane. By sensing the intracellular ADP/ATP ratio of β-cells, pancreatic K channels control insulin release and regulate ...ATP-sensitive potassium channels (K) are energy sensors on the plasma membrane. By sensing the intracellular ADP/ATP ratio of β-cells, pancreatic K channels control insulin release and regulate metabolism at the whole body level. They are implicated in many metabolic disorders and diseases and are therefore important drug targets. Here, we present three structures of pancreatic K channels solved by cryo-electron microscopy (cryo-EM), at resolutions ranging from 4.1 to 4.5 Å. These structures depict the binding site of the antidiabetic drug glibenclamide, indicate how Kir6.2 (inward-rectifying potassium channel 6.2) N-terminus participates in the coupling between the peripheral SUR1 (sulfonylurea receptor 1) subunit and the central Kir6.2 channel, reveal the binding mode of activating nucleotides, and suggest the mechanism of how Mg-ADP binding on nucleotide binding domains (NBDs) drives a conformational change of the SUR1 subunit.
History
DepositionNov 29, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update

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Structure visualization

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Assembly

Deposited unit
A: ATP-sensitive inward rectifier potassium channel 11
B: ATP-binding cassette sub-family C member 8 isoform X2
C: ATP-sensitive inward rectifier potassium channel 11
D: ATP-binding cassette sub-family C member 8 isoform X2
E: ATP-sensitive inward rectifier potassium channel 11
F: ATP-binding cassette sub-family C member 8 isoform X2
G: ATP-sensitive inward rectifier potassium channel 11
H: ATP-binding cassette sub-family C member 8 isoform X2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)887,83116
Polymers883,6458
Non-polymers4,1868
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area34700 Å2
ΔGint-315 kcal/mol
Surface area302600 Å2

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Components

#1: Protein
ATP-sensitive inward rectifier potassium channel 11 / Inward rectifier K(+) channel Kir6.2 / Potassium channel / inwardly rectifying subfamily J member 11


Mass: 43615.734 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kcnj11 / Production host: Homo sapiens (human) / References: UniProt: Q61743
#2: Protein
ATP-binding cassette sub-family C member 8 isoform X2 / SUR1


Mass: 177295.516 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesocricetus auratus (golden hamster) / Gene: Abcc8 / Production host: Homo sapiens (human) / References: UniProt: A0A1U7R319
#3: Chemical
ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: KATP / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

EM softwareName: RELION / Version: 2 / Category: 3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 6.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 11178 / Symmetry type: POINT

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