9I15 | pdb_00009i15

Crystal structure of SET cleaved after Asn175 by legumain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.47 Å
  • R-Value Free: 
    0.277 (Depositor), 0.282 (DCC) 
  • R-Value Work: 
    0.223 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 
    0.226 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Conformational and Functional Regulation of SET by Legumain Cleavage.

Horak, C.Wieland, A.C.Klaushofer, R.Briza, P.Brandstetter, H.Dall, E.

(2025) J Mol Biology 437: 169119-169119

  • DOI: https://doi.org/10.1016/j.jmb.2025.169119
  • Primary Citation of Related Structures:  
    9I15

  • PubMed Abstract: 

    The cysteine protease legumain typically localizes to the endolysosomal system, where it is an important player in the immune system. However, in the context of Alzheimer's disease (AD), legumain has been shown to be translocated to the cytosol, where it cleaves SET, synonymously termed TAF-1 or I2PP2A, an inhibitor of protein phosphatase 2A. SET is primarily found in the nucleus, where it regulates gene transcription, cell cycle progression, and histone acetylation, but can also translocate to the cytoplasm where it regulates cell migration and is implicated in neuronal apoptosis in AD. In this study, we demonstrate that legumain cleaves SET at two major sites: Asn16 at the N-terminal end and Asn175 at the earmuff domain. Contrary to previous findings, our biochemical and crystallographic experiments reveal that the corresponding N- and C-terminal cleavage products remain bound in a stable complex, rather than dissociating. Additionally, we show that the C-terminal acidic stretch of SET is essential for its binding to histone 1, and that cleavage impairs this interaction. Finally, we demonstrate that SET positively modulates PP2A activity. This effect is however abolished upon cleavage by legumain.


  • Organizational Affiliation
    • Department of Biosciences and Medical Biology, University of Salzburg 5020 Salzburg, Austria; Center of Tumor Biology and Immunology, University of Salzburg 5020 Salzburg, Austria.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 2 of Protein SETA [auth Q],
B [auth A]
209Homo sapiensMutation(s): 0 
Gene Names: SET
UniProt & NIH Common Fund Data Resources
Find proteins for Q01105 (Homo sapiens)
Explore Q01105 
Go to UniProtKB:  Q01105
PHAROS:  Q01105
GTEx:  ENSG00000119335 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ01105
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.47 Å
  • R-Value Free:  0.277 (Depositor), 0.282 (DCC) 
  • R-Value Work:  0.223 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 0.226 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.54α = 90
b = 78.17β = 91.88
c = 55.12γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Austrian Science FundAustriaY1469

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-09
    Type: Initial release