9KGA | pdb_00009kga

Crystal structure of SpTx1 toxin

  • Classification: TOXIN
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens
  • Mutation(s): No 

  • Deposited: 2024-11-08 Released: 2025-11-12 
  • Deposition Author(s): Chen, L., Wang, M., Fan, C.
  • Funding Organization(s): Ministry of Science and Technology (MoST, China), National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.214 (Depositor), 0.215 (DCC) 
  • R-Value Work: 
    0.203 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 
    0.204 (Depositor) 

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9KGA

This is version 1.2 of the entry. See complete history

Literature

Inhibition Mechanism of Pancreatic K ATP Channels by Centipede Toxin.

Hou, T.Wang, M.Tan, Y.Fan, C.Chen, L.

(2026) Research (Wash D C) 9: 1401-1401

  • DOI: https://doi.org/10.34133/research.1401
  • Primary Citation Related Structures: 
    9KGA, 9KGL

  • PubMed Abstract: 

    The pancreatic adenosine triphosphate (ATP)-sensitive potassium (K ATP ) channel acts as a crucial metabolic sensor, regulating insulin secretion to maintain whole-body energy homeostasis. Gain-of-function mutations in this channel lead to neonatal diabetes mellitus, a rare disorder in which certain mutants exhibit resistance to standard sulfonylurea therapy. Recent studies have identified a centipede toxin, SpTx1, as a potent inhibitor of both human pancreatic K ATP channels and their gain-of-function mutants. This toxin stimulates insulin secretion, offering a promising therapeutic strategy for neonatal diabetes. However, the molecular mechanism by which SpTx1 inhibits the K ATP channel has remained unclear. Here, we report the crystal structure of SpTx1 and the cryo-electron microscopy structure of the K ATP channel in complex with SpTx1. The structure reveals that a single SpTx1 molecule binds to the extracellular surface of the Kir6.2 tetramer. Multiple interactions at the SpTx1-Kir6.2 interface underpin the high affinity and specificity of SpTx1 for human Kir6.2. We demonstrate that SpTx1 inhibits potassium currents by physically blocking the ion conduction pore. Furthermore, a structure-guided search identified another centipede toxin, Sm3a, as a novel K ATP channel blocker. Together, these findings provide key insights into the inhibitory mechanism of centipede toxins against the human Kir6.2-containing K ATP channel and establish a foundation for developing these toxins into potential therapeutics for K ATP channel-related diseases.


  • Organizational Affiliation
    • State Key Laboratory of Membrane Biology, College of Future Technology, Institute of Molecular Medicine, Beijing Key Laboratory of Novel Antibodies and Multifunctional Conjugated Drugs, Peking University, Beijing 100871, China.

Macromolecule Content 

  • Total Structure Weight: 39.17 kDa 
  • Atom Count: 3,000 
  • Modeled Residue Count: 329 
  • Deposited Residue Count: 336 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
SpTx1
A, B, C, D, E
A, B, C, D, E, F
56Homo sapiensMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.214 (Depositor), 0.215 (DCC) 
  • R-Value Work:  0.203 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 0.204 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.485α = 90
b = 60.485β = 90
c = 169.854γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2022YFA1303000
National Natural Science Foundation of China (NSFC)China32225027

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-12
    Type: Initial release
  • Version 1.1: 2026-08-26
    Changes: Database references
  • Version 1.2: 2026-09-02
    Changes: Database references