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- PDB-7wit: Structure of SUR1 in complex with mitiglinide -

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Basic information

Entry
Database: PDB / ID: 7wit
TitleStructure of SUR1 in complex with mitiglinide
ComponentsATP-sensitive inward rectifier potassium channel 11,ATP-binding cassette sub-family C member 8 isoform X1
KeywordsMEMBRANE PROTEIN / SUR1 / KATP / channel / mitiglinide
Function / homology
Function and homology information


ATP sensitive Potassium channels / ATP-activated inward rectifier potassium channel activity / Regulation of insulin secretion / ABC-family proteins mediated transport / Ion homeostasis / inward rectifying potassium channel / sulfonylurea receptor activity / inward rectifier potassium channel activity / nervous system process / regulation of monoatomic ion transmembrane transport ...ATP sensitive Potassium channels / ATP-activated inward rectifier potassium channel activity / Regulation of insulin secretion / ABC-family proteins mediated transport / Ion homeostasis / inward rectifying potassium channel / sulfonylurea receptor activity / inward rectifier potassium channel activity / nervous system process / regulation of monoatomic ion transmembrane transport / ankyrin binding / response to ATP / potassium ion import across plasma membrane / negative regulation of insulin secretion / ABC-type transporter activity / regulation of membrane potential / potassium ion transport / glucose metabolic process / transmembrane transporter binding / membrane => GO:0016020 / response to xenobiotic stimulus / ATP binding / plasma membrane
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 / ABC transporter transmembrane region ...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
Chem-9I0 / ADENOSINE-5'-TRIPHOSPHATE / ATP-binding cassette sub-family C member 8 isoform X1 / ATP-sensitive inward rectifier potassium channel 11
Similarity search - Component
Biological speciesBos taurus (cattle)
Mesocricetus auratus (golden hamster)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.21 Å
AuthorsChen, L. / Wang, M.M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)91957201 and 31870833 China
CitationJournal: Front Pharmacol / Year: 2022
Title: Structural Insights Into the High Selectivity of the Anti-Diabetic Drug Mitiglinide.
Authors: Mengmeng Wang / Jing-Xiang Wu / Lei Chen /
Abstract: Mitiglinide is a highly selective fast-acting anti-diabetic drug that induces insulin secretion by inhibiting pancreatic K channels. However, how mitiglinide binds K channels remains unknown. Here, ...Mitiglinide is a highly selective fast-acting anti-diabetic drug that induces insulin secretion by inhibiting pancreatic K channels. However, how mitiglinide binds K channels remains unknown. Here, we show the cryo-EM structure of the SUR1 subunit complexed with mitiglinide. The structure reveals that mitiglinide binds inside the common insulin secretagogue-binding site of SUR1, which is surrounded by TM7, TM8, TM16, and TM17. Mitiglinide locks SUR1 in the NBD-separated inward-facing conformation. The detailed structural analysis of the mitiglinide-binding site uncovers the molecular basis of its high selectivity.
History
DepositionJan 4, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2022Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-sensitive inward rectifier potassium channel 11,ATP-binding cassette sub-family C member 8 isoform X1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,2623
Polymers159,4401
Non-polymers8232
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ATP-sensitive inward rectifier potassium channel 11,ATP-binding cassette sub-family C member 8 isoform X1 / Inward rectifier K(+) channel Kir6.2 / Potassium channel / inwardly rectifying subfamily J member 11


Mass: 159439.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Fusion protein of potassium channel, linkers and Abcc8
Source: (gene. exp.) Bos taurus (cattle), (gene. exp.) Mesocricetus auratus (golden hamster)
Gene: KCNJ11, Abcc8 / Production host: Homo sapiens (human) / References: UniProt: A2VDS4, UniProt: A0A1U8CME7
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-9I0 / (2S)-4-[(3aR,7aS)-1,3,3a,4,5,6,7,7a-octahydroisoindol-2-yl]-4-oxidanylidene-2-(phenylmethyl)butanoic acid / Mitiglinide / Mitiglinide


Mass: 315.407 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H25NO3 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: Sulfonylurea receptor 1 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Mesocricetus auratus (golden hamster)
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 FIELDBright-field microscopy / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: DIRECT ELECTRON DE-16 (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.21 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 82717 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0058262
ELECTRON MICROSCOPYf_angle_d0.49911298
ELECTRON MICROSCOPYf_dihedral_angle_d10.9682708
ELECTRON MICROSCOPYf_chiral_restr0.041401
ELECTRON MICROSCOPYf_plane_restr0.0031408

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