4WJN

Crystal structure of SUMO1 in complex with phosphorylated PML


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.158 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural and Functional Characterization of the Phosphorylation-Dependent Interaction between PML and SUMO1.

Cappadocia, L.Mascle, X.H.Bourdeau, V.Tremblay-Belzile, S.Chaker-Margot, M.Lussier-Price, M.Wada, J.Sakaguchi, K.Aubry, M.Ferbeyre, G.Omichinski, J.G.

(2015) Structure 23: 126-138

  • DOI: 10.1016/j.str.2014.10.015
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • PML and several other proteins localizing in PML-nuclear bodies (PML-NB) contain phosphoSIMs (SUMO-interacting motifs), and phosphorylation of this motif plays a key role in their interaction with SUMO family proteins. We examined the role that phosp ...

    PML and several other proteins localizing in PML-nuclear bodies (PML-NB) contain phosphoSIMs (SUMO-interacting motifs), and phosphorylation of this motif plays a key role in their interaction with SUMO family proteins. We examined the role that phosphorylation plays in the binding of the phosphoSIMs of PML and Daxx to SUMO1 at the atomic level. The crystal structures of SUMO1 bound to unphosphorylated and tetraphosphorylated PML-SIM peptides indicate that three phosphoserines directly contact specific positively charged residues of SUMO1. Surprisingly, the crystal structure of SUMO1 bound to a diphosphorylated Daxx-SIM peptide indicate that the hydrophobic residues of the phosphoSIM bind in a manner similar to that seen with PML, but important differences are observed when comparing the phosphorylated residues. Together, the results provide an atomic level description of how specific acetylation patterns within different SUMO family proteins can work together with phosphorylation of phosphoSIM's regions of target proteins to regulate binding specificity.


    Organizational Affiliation

    Département de Biochimie et Médicine Moléculaire, Université de Montréal, C.P. 6128 Succursale Centre-Ville, Montréal, QC H3C 3J7, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Small ubiquitin-related modifier 1
A
83Homo sapiensMutation(s): 1 
Gene Names: SUMO1 (SMT3C, SMT3H3, UBL1)
Find proteins for P63165 (Homo sapiens)
Go to Gene View: SUMO1
Go to UniProtKB:  P63165
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Protein PML
B
29Homo sapiensMutation(s): 0 
Gene Names: PML (MYL, PP8675, RNF71, TRIM19)
Find proteins for P29590 (Homo sapiens)
Go to Gene View: PML
Go to UniProtKB:  P29590
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
B
L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.158 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 38.274α = 90.00
b = 47.079β = 90.00
c = 63.986γ = 90.00
Software Package:
Software NamePurpose
Cootmodel building
XSCALEdata scaling
XDSdata reduction
PHENIXrefinement
CBASSdata collection
PHENIXphasing
SCALAdata scaling
XDSdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-12-31
    Type: Initial release
  • Version 1.1: 2015-01-14
    Type: Database references
  • Version 1.2: 2017-11-22
    Type: Database references, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary