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- PDB-6jb3: Structure of SUR1 subunit bound with repaglinide -

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Basic information

Entry
Database: PDB / ID: 6jb3
TitleStructure of SUR1 subunit bound with repaglinide
ComponentsATP-binding cassette sub-family C member 8 isoform X2
KeywordsMEMBRANE PROTEIN / KATP / channel / repaglinide / Kir / ABC transporter / SUR / diabetes / insulin secretagogue
Function / homology
Function and homology information


glutamate secretion, neurotransmission / inward rectifying potassium channel / sulfonylurea receptor activity / ATPase-coupled monoatomic cation transmembrane transporter activity / : / neuromuscular process / action potential / potassium channel activity / positive regulation of insulin secretion involved in cellular response to glucose stimulus / ABC-type transporter activity ...glutamate secretion, neurotransmission / inward rectifying potassium channel / sulfonylurea receptor activity / ATPase-coupled monoatomic cation transmembrane transporter activity / : / neuromuscular process / action potential / potassium channel activity / positive regulation of insulin secretion involved in cellular response to glucose stimulus / ABC-type transporter activity / cellular response to nutrient levels / negative regulation of insulin secretion / 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 ...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
Repaglinide / ATP-binding cassette sub-family C member 8
Similarity search - Component
Biological speciesMesocricetus auratus (golden hamster)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.53 Å
AuthorsChen, L. / Ding, D. / Wang, M. / Wu, J.-X. / Kang, Y.
Funding support China, 4items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2016YFA0502004 China
National Natural Science Foundation of China31622021 China
National Natural Science Foundation of China31821091 China
National Natural Science Foundation of China31870833 China
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, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB
Revision 2.0Sep 29, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references
Category: atom_site / database_2 ...atom_site / database_2 / database_PDB_caveat / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.type_symbol / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id
Revision 2.1May 29, 2024Group: Data collection / Refinement description / Category: chem_comp_atom / chem_comp_bond / refine / Item: _refine.ls_d_res_high / _refine.ls_d_res_low

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Structure visualization

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Assembly

Deposited unit
B: ATP-binding cassette sub-family C member 8 isoform X2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,9773
Polymers177,2961
Non-polymers1,6822
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ATP-binding cassette sub-family C member 8 isoform X2 / SUR1


Mass: 177295.516 Da / Num. of mol.: 1
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
#2: Chemical ChemComp-BJX / Repaglinide / 2-ethoxy-4-[2-({(1S)-3-methyl-1-[2-(piperidin-1-yl)phenyl]butyl}amino)-2-oxoethyl]benzoic acid


Mass: 452.586 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H36N2O4
#3: Chemical ChemComp-AJP / Digitonin


Mass: 1229.312 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C56H92O29 / Comment: detergent*YM

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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: SUR1 / Type: COMPLEX / Entity ID: #1 / 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

SoftwareName: PHENIX / Version: (1.12_2829: ???) / Classification: refinement
EM softwareName: RELION / Version: 2 / Category: 3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.53 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 653991 / Symmetry type: POINT
RefinementResolution: 3.53→3.53 Å / SU ML: 1.4 / σ(F): 0.01 / Phase error: 64.36 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.403 2069 2.25 %
Rwork0.3913 --
obs0.3916 91922 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0045470
ELECTRON MICROSCOPYf_angle_d0.8217449
ELECTRON MICROSCOPYf_dihedral_angle_d17.5263258
ELECTRON MICROSCOPYf_chiral_restr0.042930
ELECTRON MICROSCOPYf_plane_restr0.005879
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0007-3.07050.78621270.86696037ELECTRON MICROSCOPY99
3.0705-3.14730.95771430.92765878ELECTRON MICROSCOPY99
3.1473-3.23240.01011080.95826071ELECTRON MICROSCOPY99
3.2324-3.32750.94231560.97925934ELECTRON MICROSCOPY100
3.3275-3.43490.8041200.87375908ELECTRON MICROSCOPY100
3.4349-3.55760.61121320.61116002ELECTRON MICROSCOPY100
3.5576-3.70010.5811560.53666048ELECTRON MICROSCOPY100
3.7001-3.86850.47181080.48195977ELECTRON MICROSCOPY100
3.8685-4.07240.46571320.43996165ELECTRON MICROSCOPY100
4.0724-4.32750.40251560.37995884ELECTRON MICROSCOPY100
4.3275-4.66160.33341320.33866001ELECTRON MICROSCOPY100
4.6616-5.13060.35741080.3295940ELECTRON MICROSCOPY100
5.1306-5.87280.44961680.42886077ELECTRON MICROSCOPY100
5.8728-7.39810.4171440.42016043ELECTRON MICROSCOPY100
7.3981-74.92010.3561790.34475888ELECTRON MICROSCOPY100

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