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- PDB-9dfx: Cryo-EM structure of a SUR1/Kir6.2 ATP-sensitive potassium channe... -

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Basic information

Entry
Database: PDB / ID: 9dfx
TitleCryo-EM structure of a SUR1/Kir6.2 ATP-sensitive potassium channel in the presence of Aekatperone in the closed conformation
Components
  • ATP-sensitive inward rectifier potassium channel 11
  • SUR1
KeywordsTRANSPORT PROTEIN / ATP-sensitive potassium channel / KATP channel / SUR1 / Kir6.2 / potassium transport / metabolic sensor / congenital hyperinsulinism / trafficking / pharmacochaperone
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 / ventricular cardiac muscle tissue development / cell body fiber / 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 / ventricular cardiac muscle tissue development / cell body fiber / CAMKK-AMPK signaling cascade / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / inward rectifier potassium channel activity / ATPase-coupled monoatomic cation transmembrane transporter activity / regulation of monoatomic ion transmembrane transport / nervous system process / inorganic cation transmembrane transport / ankyrin binding / Ion homeostasis / response to ATP / response to stress / potassium ion import across plasma membrane / response to testosterone / action potential / voltage-gated potassium channel activity / axolemma / intercalated disc / ABC-type transporter activity / cellular response to nutrient levels / negative regulation of insulin secretion / heat shock protein binding / potassium ion transmembrane transport / T-tubule / regulation of insulin secretion / acrosomal vesicle / response to ischemia / regulation of membrane potential / determination of adult lifespan / positive regulation of protein localization to plasma membrane / cellular response to glucose stimulus / potassium ion transport / sarcolemma / 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 / metal ion 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
: / ADENOSINE-5'-TRIPHOSPHATE / : / SUR1 / ATP-sensitive inward rectifier potassium channel 11
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Mesocricetus auratus (golden hamster)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsDriggers, C.M. / ElSheikh, A. / Shyng, S.-L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK066485 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM129547 United States
Citation
Journal: Elife / Year: 2025
Title: AI-based discovery and cryoEM structural elucidation of a K channel pharmacochaperone.
Authors: Assmaa Elsheikh / Camden M Driggers / Ha H Truong / Zhongying Yang / John Allen / Niel M Henriksen / Katarzyna Walczewska-Szewc / Show-Ling Shyng /
Abstract: Pancreatic K channel trafficking defects underlie congenital hyperinsulinism (CHI) cases unresponsive to the K channel opener diazoxide, the mainstay medical therapy for CHI. Current clinically used ...Pancreatic K channel trafficking defects underlie congenital hyperinsulinism (CHI) cases unresponsive to the K channel opener diazoxide, the mainstay medical therapy for CHI. Current clinically used K channel inhibitors have been shown to act as pharmacochaperones and restore surface expression of trafficking mutants; however, their therapeutic utility for K trafficking-impaired CHI is hindered by high affinity binding, which limits functional recovery of rescued channels. Recent structural studies of K channels employing cryo-electron microscopy (cryoEM) have revealed a promiscuous pocket where several known K pharmacochaperones bind. The structural knowledge provides a framework for discovering K channel pharmacochaperones with desired reversible inhibitory effects to permit functional recovery of rescued channels. Using an AI-based virtual screening technology AtomNet followed by functional validation, we identified a novel compound, termed Aekatperone, which exhibits chaperoning effects on K channel trafficking mutations. Aekatperone reversibly inhibits K channel activity with a half-maximal inhibitory concentration (IC) ~9 μM. Mutant channels rescued to the cell surface by Aekatperone showed functional recovery upon washout of the compound. CryoEM structure of K bound to Aekatperone revealed distinct binding features compared to known high affinity inhibitor pharmacochaperones. Our findings unveil a K pharmacochaperone enabling functional recovery of rescued channels as a promising therapeutic for CHI caused by K trafficking defects.
#1: Journal: Elife / Year: 2024
Title: AI-Based Discovery and CryoEM Structural Elucidation of a KATP Channel Pharmacochaperone
Authors: ElSheikh, A. / Driggers, C.M. / Truong, H.H. / Yang, Z. / Allen, J. / Henriksen, N. / Walczewska-Szewc, K. / Shyng, S.L.
History
DepositionAug 30, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP-sensitive inward rectifier potassium channel 11
E: SUR1
B: ATP-sensitive inward rectifier potassium channel 11
C: ATP-sensitive inward rectifier potassium channel 11
D: ATP-sensitive inward rectifier potassium channel 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)355,33518
Polymers351,9445
Non-polymers3,39113
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid 31 through 401)
d_2ens_1(chain "B" and resid 31 through 401)
d_3ens_1(chain "C" and resid 31 through 401)
d_4ens_1chain "D"

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ARGARGTHRTHRAA31 - 36031 - 360
d_12ATPATPATPATPAF401
d_21ARGARGTHRTHRBC31 - 36031 - 360
d_22ATPATPATPATPBM401
d_31ARGARGTHRTHRCD31 - 36031 - 360
d_32ATPATPATPATPCN401
d_41ARGARGTHRTHRDE31 - 36031 - 360
d_42ATPATPATPATPDR402

NCS oper:
IDCodeMatrixVector
1given(-0.00563463434845, 0.99998362876, 0.000996547889498), (-0.9999750978, -0.00563034613736, -0.00425475995244), (-0.00424907938719, -0.00102049708984, 0.999990451909)1.05408251132, 541.191763077, 1.35723284756
2given(-0.999907372098, -0.012348598823, -0.00572357678575), (0.0123613557593, -0.99992117787, -0.00219884753933), (-0.00569597295511, -0.00226939503356, 0.999981202692)542.992717482, 535.853486981, 2.25008101076
3given(0.000100208513615, -0.999998972123, -0.00143028388835), (0.999998926948, 9.81179060275E-5, 0.00146166850448), (-0.00146152666561, -0.00143042882521, 0.999997908904)538.768074367, -0.0923428612551, 0.852906133738

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Components

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Protein , 2 types, 5 molecules ABCDE

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


Mass: 43661.762 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Kcnj11 / Cell line (production host): INS-1 / Production host: Rattus norvegicus (Norway rat) / References: UniProt: P70673
#2: Protein SUR1


Mass: 177296.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesocricetus auratus (golden hamster) / Cell: Beta Cell / Organ: pancreas / Cell line (production host): INS-1 / Production host: Rattus norvegicus (Norway rat) / References: UniProt: A0A1S4NYG1

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Sugars , 1 types, 1 molecules

#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 12 molecules

#3: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-A1A4F / N-[3-(cyclohexylmethyl)-1H-pyrazol-5-yl]-2-[(1H-imidazol-1-yl)methyl]benzene-1-sulfonamide


Mass: 399.510 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H25N5O2S / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
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: Kir6.2/SUR1 closed channel in complex with Aekatperone
Type: COMPLEX
Details: Kir6.2/SUR1 KATP channel in the closed conformation in complex with ATP and Aekatperone
Entity ID: #1-#2 / Source: MULTIPLE SOURCES
Molecular weightValue: 0.880 MDa / Experimental value: NO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Source (recombinant)Organism: Rattus norvegicus (Norway rat) / Cell: INS-1 cells / Plasmid: recombinant adenovirus
Buffer solutionpH: 7.4 / Details: MSB with GDN, ATP and AKP
Buffer component
IDConc.NameFormulaBuffer-ID
1200 mMsodium chlorideNaCl1
2100 mMpotassium chlorideKCl1
350 mMHEPES pH 7.51
41 mMATP1
50.05 %GDN1
60.05 mMAekatperone1
SpecimenConc.: 0.15 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Three microliters of purified Kir6.2-Q52R/FLAG-SUR1 were loaded onto Quantifoil R 1.2/1.3 Au 300 grids prepared with a fresh graphene oxide surface.
Specimen supportGrid type: EMS Lacey Carbon
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 279 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Details: Titan Krios with Falcon K3 at the Pacific Northwest National Lab
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 3.2 sec. / Electron dose: 55 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 2 / Num. of real images: 21012

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.2.1particle selection
2SerialEMimage acquisition
4cryoSPARC4.2.1CTF correction
7Cootmodel fitting
9cryoSPARC4.2.1initial Euler assignment
10cryoSPARC4.2.1final Euler assignment
11cryoSPARC4.2.1classification
12cryoSPARC4.2.13D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 78490
3D reconstructionResolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 78490 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT
Atomic model buildingPDB-ID: 7TYS

7tys


Accession code: 7TYS / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 283.62 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.001320522
ELECTRON MICROSCOPYf_angle_d0.362228131
ELECTRON MICROSCOPYf_chiral_restr0.03853438
ELECTRON MICROSCOPYf_plane_restr0.00273528
ELECTRON MICROSCOPYf_dihedral_angle_d7.8756684
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAELECTRON MICROSCOPYNCS constraints3.68648949269E-10
ens_1d_3AAELECTRON MICROSCOPYNCS constraints2.26609059648E-11
ens_1d_4AAELECTRON MICROSCOPYNCS constraints3.82319038263E-10

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