9GZ6 | pdb_00009gz6

WT-IAPP cryo-EM structure Type SS - control reaction


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Kinetic Steering of Amyloid Formation and Polymorphism by Canagliflozin, a Type-2 Diabetes Drug.

Taylor, A.I.P.Xu, Y.Wilkinson, M.Chakraborty, P.Brinkworth, A.Willis, L.F.Zhuravleva, A.Ranson, N.A.Foster, R.Radford, S.E.

(2025) J Am Chem Soc 147: 11859-11878

  • DOI: https://doi.org/10.1021/jacs.4c16743
  • Primary Citation of Related Structures:  
    9GZ6, 9GZP, 9GZS, 9GZT, 9GZW, 9GZX, 9GZY

  • PubMed Abstract: 

    Amyloid formation is involved in widespread health conditions such as Alzheimer's disease, Parkinson's disease, and type-2 diabetes. Amyloid fibrils have a similar cross-β architecture, but fibrils formed by a single protein sequence can have diverse structures, varying with time, self-assembly conditions, and sequence modifications. Fibril structure has been proposed to be diagnostic of disease, but why different structures result under different conditions, especially in vitro, remains elusive. We previously identified a small molecule, YX-I-1, which inhibits in vitro amyloid formation by islet amyloid polypeptide (IAPP), a peptide hormone whose amyloid formation is involved in type-2 diabetes. Here, using YX-I-1 as a lead, we identified regulator-approved drugs with similar structures by chemical similarity analysis and substructure searches and monitored the effect of 24 of these potential ligands on IAPP amyloid assembly in vitro. We show that one such compound, canagliflozin (Invokana), a type-2 diabetes drug already in clinical use, can strongly delay the kinetics of IAPP amyloid formation, an activity independent of its intended mode of action [sodium-glucose linked transporter 2 (SGLT2) inhibitor] that may have important therapeutic implications. Combining analysis of amyloid self-assembly kinetics, biophysical characterization of monomer and fibril binding, and cryo-EM of the assembly products, we show that YX-I-1 and canagliflozin target IAPP early in aggregation, remodeling the energy landscape of primary nucleation and profoundly altering the resulting fibril structures. Early binding events thus imprint long-lasting effects on the amyloid structures that form.


  • Organizational Affiliation
    • Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, LS2 9JT Leeds, U.K.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Islet amyloid polypeptide
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
38Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P10997 (Homo sapiens)
Explore P10997 
Go to UniProtKB:  P10997
PHAROS:  P10997
GTEx:  ENSG00000121351 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10997
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION4
MODEL REFINEMENTPHENIX1.17.1_3660:

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom204963
Royal SocietyUnited KingdomRSRP/R1/211057

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-05
    Type: Initial release
  • Version 1.1: 2025-04-16
    Changes: Data collection, Database references