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- PDB-9kgl: Structure of KATP channel in complex with centipede toxin SpTx1 -

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Basic information

Entry
Database: PDB / ID: 9kgl
TitleStructure of KATP channel in complex with centipede toxin SpTx1
Components
  • ATP-binding cassette sub-family C member 8 isoform X2
  • ATP-sensitive inward rectifier potassium channel 11
  • SpTx1
KeywordsTRANSPORT PROTEIN / KATP / Kir6.2 / SUR1 / Glibenclamide / SpTx1
Function / homology
Function and homology information


Defective ABCC9 causes CMD10, ATFB12 and Cantu syndrome / ATP sensitive Potassium channels / Defective ABCC8 can cause hypo- and hyper-glycemias / ATP-activated inward rectifier potassium channel activity / glutamate secretion, neurotransmission / response to resveratrol / inward rectifying potassium channel / sulfonylurea receptor activity / ventricular cardiac muscle tissue development / CAMKK-AMPK signaling cascade ...Defective ABCC9 causes CMD10, ATFB12 and Cantu syndrome / ATP sensitive Potassium channels / Defective ABCC8 can cause hypo- and hyper-glycemias / ATP-activated inward rectifier potassium channel activity / glutamate secretion, neurotransmission / response to resveratrol / inward rectifying potassium channel / sulfonylurea receptor activity / ventricular cardiac muscle tissue development / CAMKK-AMPK signaling cascade / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / regulation of monoatomic ion transmembrane transport / ATPase-coupled monoatomic cation transmembrane transporter activity / nervous system process / : / ankyrin binding / neuromuscular process / response to ATP / potassium ion import across plasma membrane / potassium ion binding / action potential / voltage-gated potassium channel activity / potassium channel activity / positive regulation of insulin secretion involved in cellular response to glucose stimulus / ABC-type transporter activity / cellular response to nutrient levels / Ion homeostasis / potassium ion transmembrane transport / T-tubule / regulation of insulin secretion / response to ischemia / determination of adult lifespan / regulation of membrane potential / Regulation of insulin secretion / negative regulation of insulin secretion / ADP binding / sarcolemma / ABC-family proteins mediated transport / glucose metabolic process / presynapse / transmembrane transporter binding / response to hypoxia / response to xenobiotic stimulus / apoptotic process / 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 / Chem-GBM / ATP-binding cassette sub-family C member 8 / ATP-sensitive inward rectifier potassium channel 11
Similarity search - Component
Biological speciesHomo sapiens (human)
Mesocricetus auratus (golden hamster)
Scolopendra polymorpha (arthropod)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.88 Å
AuthorsChen, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)91957201 China
CitationJournal: To Be Published
Title: Structure of KATP in complex with SpTx1
Authors: Chen, L. / Wang, M.
History
DepositionNov 8, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 12, 2025Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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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
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
I: SpTx1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)896,12621
Polymers890,0939
Non-polymers6,03312
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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


Mass: 43595.723 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KCNJ11 / Production host: Homo sapiens (human) / References: UniProt: Q14654
#2: Protein
ATP-binding cassette sub-family C member 8 isoform X2


Mass: 177295.594 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: Protein SpTx1


Mass: 6527.552 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Scolopendra polymorpha (arthropod) / Production host: Escherichia coli (E. coli)
#4: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical
ChemComp-GBM / 5-chloro-N-(2-{4-[(cyclohexylcarbamoyl)sulfamoyl]phenyl}ethyl)-2-methoxybenzamide / Glibenclamide / Glyburide


Mass: 494.004 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C23H28ClN3O5S
Has ligand of interestN
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 in complex with SpTx1 / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 2.88 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 246583 / Symmetry type: POINT

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