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- PDB-5wua: Structure of a Pancreatic ATP-sensitive Potassium Channel -

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Basic information

Entry
Database: PDB / ID: 5wua
TitleStructure of a Pancreatic ATP-sensitive Potassium Channel
Components
  • ATP-sensitive inward rectifier potassium channel 11,superfolder GFP
  • SUR1
KeywordsTRANSPORT PROTEIN / KATP / channel / ABC transporter / Kir
Function / homology
Function and homology information


ATP sensitive Potassium channels / response to resveratrol / ATP-activated inward rectifier potassium channel activity / inward rectifying potassium channel / Regulation of insulin secretion / sulfonylurea receptor activity / cell body fiber / ventricular cardiac muscle tissue development / ABC-family proteins mediated transport / CAMKK-AMPK signaling cascade ...ATP sensitive Potassium channels / response to resveratrol / ATP-activated inward rectifier potassium channel activity / inward rectifying potassium channel / Regulation of insulin secretion / sulfonylurea receptor activity / cell body fiber / ventricular cardiac muscle tissue development / ABC-family proteins mediated transport / CAMKK-AMPK signaling cascade / inward rectifier potassium channel activity / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / Ion homeostasis / ATPase-coupled monoatomic cation transmembrane transporter activity / nervous system process / inorganic cation transmembrane transport / ankyrin binding / response to ATP / response to stress / potassium ion import across plasma membrane / response to testosterone / potassium ion binding / action potential / intercalated disc / axolemma / negative regulation of insulin secretion / cellular response to nutrient levels / ABC-type transporter activity / T-tubule / heat shock protein binding / acrosomal vesicle / response to ischemia / determination of adult lifespan / positive regulation of protein localization to plasma membrane / cellular response to glucose stimulus / potassium ion transport / cellular response to nicotine / glucose metabolic process / nuclear envelope / cellular response to tumor necrosis factor / response to estradiol / presynaptic membrane / transmembrane transporter binding / response to hypoxia / endosome / response to xenobiotic stimulus / neuronal cell body / apoptotic process / glutamatergic synapse / protein-containing complex / 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
SUR1 / ATP-sensitive inward rectifier potassium channel 11
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
Mesocricetus auratus (golden hamster)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.6 Å
AuthorsLi, N. / Wu, J.-X. / Chen, L. / Gao, N.
Funding support China, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology of China2016YFA0502004,2016YFA0500700,2013CB910404 China
National Natural Science Foundation of China31622021, 31521062,31422016, 31470722, 31630087 China
CitationJournal: Cell / Year: 2017
Title: Structure of a Pancreatic ATP-Sensitive Potassium Channel.
Authors: Ningning Li / Jing-Xiang Wu / Dian Ding / Jiaxuan Cheng / Ning Gao / Lei Chen /
Abstract: ATP-sensitive potassium channels (K) couple intracellular ATP levels with membrane excitability. These channels play crucial roles in many essential physiological processes and have been implicated ...ATP-sensitive potassium channels (K) couple intracellular ATP levels with membrane excitability. These channels play crucial roles in many essential physiological processes and have been implicated extensively in a spectrum of metabolic diseases and disorders. To gain insight into the mechanism of K, we elucidated the structure of a hetero-octameric pancreatic K channel in complex with a non-competitive inhibitor glibenclamide by single-particle cryoelectron microscopy to 5.6-Å resolution. The structure shows that four SUR1 regulatory subunits locate peripherally and dock onto the central Kir6.2 channel tetramer through the SUR1 TMD0-L0 fragment. Glibenclamide-bound SUR1 uses TMD0-L0 fragment to stabilize Kir6.2 channel in a closed conformation. In another structural population, a putative co-purified phosphatidylinositol 4,5-bisphosphate (PIP) molecule uncouples Kir6.2 from glibenclamide-bound SUR1. These structural observations suggest a molecular mechanism for K regulation by anti-diabetic sulfonylurea drugs, intracellular adenosine nucleotide concentrations, and PIP lipid.
History
DepositionDec 16, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / em_image_scans / em_software / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _em_software.name

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Assembly

Deposited unit
A: ATP-sensitive inward rectifier potassium channel 11,superfolder GFP
B: ATP-sensitive inward rectifier potassium channel 11,superfolder GFP
C: ATP-sensitive inward rectifier potassium channel 11,superfolder GFP
D: ATP-sensitive inward rectifier potassium channel 11,superfolder GFP
E: SUR1
F: SUR1
G: SUR1
H: SUR1


Theoretical massNumber of molelcules
Total (without water)1,014,5438
Polymers1,014,5438
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area29820 Å2
ΔGint-266 kcal/mol
Surface area348440 Å2

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Components

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


Mass: 76339.242 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: ATP-sensitive inward rectifier potassium channel 11 with C-terminal synthetic superfolder GFP and affinity tags added
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) synthetic construct (others)
Gene: Kcnj11 / Cell line (production host): HEK / Production host: Homo sapiens (human) / References: UniProt: Q61743
#2: Protein
SUR1 / Sulfonylurea receptor 1


Mass: 177296.578 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesocricetus auratus (golden hamster) / Cell line (production host): HEK / Production host: Homo sapiens (human) / References: UniProt: A0A1S4NYG1*PLUS
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

Component
IDNameTypeEntity IDParent-IDSource
1ATP sensitive potassiumCOMPLEXall0RECOMBINANT
2ATP-sensitive inward rectifier potassium channel 11COMPLEX#11RECOMBINANT
3SUR1COMPLEX#21RECOMBINANT
Molecular weightValue: 880 kDa/nm / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Mus musculus (house mouse)10090
31Mesocricetus auratus (golden hamster)10036
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDCellPlasmid
21Homo sapiens (human)9606HEKBacMam
31Homo sapiens (human)9606HEK
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: 40 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

EM softwareName: RELION / Version: 2 / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 5.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 34500 / Symmetry type: POINT

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