8DJH

Ternary complex of SUMO1 with a phosphomimetic SIM of PML and zinc


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.216 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Zinc controls PML nuclear body formation through regulation of a paralog specific auto-inhibition in SUMO1.

Lussier-Price, M.Wahba, H.M.Mascle, X.H.Cappadocia, L.Bourdeau, V.Gagnon, C.Igelmann, S.Sakaguchi, K.Ferbeyre, G.Omichinski, J.G.

(2022) Nucleic Acids Res 50: 8331-8348

  • DOI: https://doi.org/10.1093/nar/gkac620
  • Primary Citation of Related Structures:  
    8DJH, 8DJI

  • PubMed Abstract: 

    SUMO proteins are important regulators of many key cellular functions in part through their ability to form interactions with other proteins containing SUMO interacting motifs (SIMs). One characteristic feature of all SUMO proteins is the presence of a highly divergent intrinsically disordered region at their N-terminus. In this study, we examine the role of this N-terminal region of SUMO proteins in SUMO-SIM interactions required for the formation of nuclear bodies by the promyelocytic leukemia (PML) protein (PML-NBs). We demonstrate that the N-terminal region of SUMO1 functions in a paralog specific manner as an auto-inhibition domain by blocking its binding to the phosphorylated SIMs of PML and Daxx. Interestingly, we find that this auto-inhibition in SUMO1 is relieved by zinc, and structurally show that zinc stabilizes the complex between SUMO1 and a phospho-mimetic form of the SIM of PML. In addition, we demonstrate that increasing cellular zinc levels enhances PML-NB formation in senescent cells. Taken together, these results provide important insights into a paralog specific function of SUMO1, and suggest that zinc levels could play a crucial role in regulating SUMO1-SIM interactions required for PML-NB formation and function.


  • Organizational Affiliation

    Département de Biochimie et Médicine Moléculaire, Université de Montréal, Montréal, QC, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Small ubiquitin-related modifier 197Homo sapiensMutation(s): 0 
Gene Names: SUMO1SMT3CSMT3H3UBL1OK/SW-cl.43
UniProt & NIH Common Fund Data Resources
Find proteins for P63165 (Homo sapiens)
Explore P63165 
Go to UniProtKB:  P63165
PHAROS:  P63165
GTEx:  ENSG00000116030 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63165
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PML 4SD29Homo sapiensMutation(s): 0 
EC: 2.3.2
UniProt & NIH Common Fund Data Resources
Find proteins for P29590 (Homo sapiens)
Explore P29590 
Go to UniProtKB:  P29590
PHAROS:  P29590
GTEx:  ENSG00000140464 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29590
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.216 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.776α = 90
b = 47.46β = 90
c = 63.632γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)Canada70439, 130414 and 166104

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-10
    Type: Initial release
  • Version 1.1: 2022-08-24
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description