Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: isothermal titration calorimetry

Macromolecule Content

• Total Structure Weight: 12.86 kDa 
• Atom Count: 856 
• Residue Count: 92 
• Unique protein chains: 2

6UYT

Crystal structure of K39-acetylated SUMO1 in complex with phosphorylated PML-SIM

• DOI: 10.2210/pdb6UYT/pdb

• Classification: NUCLEAR PROTEIN/PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2019-11-14 Released: 2019-11-27 
• Deposition Author(s): Wahba, H.M., Gagnon, C., Mascle, X.H., Lussier-Price, M., Cappadocia, L., Sakaguchi, K., Omichinski, J.G.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free: 0.200 
• R-Value Work: 0.171 
• R-Value Observed: 0.174 

Literature

Acetylation of SUMO1 Alters Interactions with the SIMs of PML and Daxx in a Protein-Specific Manner.

Mascle, X.H., Gagnon, C., Wahba, H.M., Lussier-Price, M., Cappadocia, L., Sakaguchi, K., Omichinski, J.G.

(2020) Structure 28: 157-168.e5

• PubMed: 31879127 
• DOI: 10.1016/j.str.2019.11.019
• Primary Citation of Related Structures:  
  6UYS, 6UYR, 6UYU, 6UYT, 6UYV, 6UYY, 6UYX, 6UYO, 6UYQ, 6UYP


• PubMed Abstract: 
  

The interactions between SUMO proteins and SUMO-interacting motif (SIM) in nuclear bodies formed by the promyelocytic leukemia (PML) protein (PML-NBs) have been shown to be modulated by either phosphorylation of the SIMs or acetylation of SUMO proteins. However, little is known about how this occurs at the atomic level. In this work, we examined the role that acetylation of SUMO1 plays on its binding to the phosphorylated SIMs (phosphoSIMs) of PML and Daxx. Our results demonstrate that SUMO1 binding to the phosphoSIM of either PML or Daxx is dramatically reduced by acetylation at either K39 or K46. However, acetylation at K37 only impacts binding to Daxx. Structures of acetylated SUMO1 variants bound to the phosphoSIMs of PML and Daxx demonstrate that there is structural plasticity in SUMO-SIM interactions. The plasticity observed in these structures provides a robust mechanism for regulating SUMO-SIM interactions in PML-NBs using signaling generated post-translational modifications.

---

Organizational Affiliation: 

Département de Biochimie et Médicine Moléculaire, Université de Montréal, C.P. 6128 Succursale Centre-Ville, Montréal, QC H3C 3J7, Canada. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ubiquitin-related modifier 1	A	83	Homo sapiens	Mutation(s): 1  Gene Names: SUMO1, SMT3C, SMT3H3, UBL1, OK/SW-cl.43
Find proteins for P63165 (Homo sapiens) Explore P63165  Go to UniProtKB:  P63165
NIH Common Fund Data Resources
PHAROS  P63165 GTEx  ENSG00000116030

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein PML	B	29	Homo sapiens	Mutation(s): 1  Gene Names: PML, MYL, PP8675, RNF71, TRIM19
Find proteins for P29590 (Homo sapiens) Explore P29590  Go to UniProtKB:  P29590
NIH Common Fund Data Resources
PHAROS  P29590 GTEx  ENSG00000140464

Small Molecules

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ALY	A	L-PEPTIDE LINKING	C8 H16 N2 O3		LYS
SEP	B	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free: 0.200 
• R-Value Work: 0.171 
• R-Value Observed: 0.174 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.458	α = 90
b = 46.942	β = 90
c = 62.385	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2019-11-14 
• Released Date: 2019-11-27 
Deposition Author(s): Wahba, H.M., Gagnon, C., Mascle, X.H., Lussier-Price, M., Cappadocia, L., Sakaguchi, K., Omichinski, J.G.

---

Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	74739
Canadian Institutes of Health Research (CIHR)	Canada	130414

Revision History 

• Version 1.0: 2019-11-27
  Type: Initial release
  
• Version 1.1: 2020-01-08
  Changes: Author supporting evidence, Database references
• Version 1.2: 2020-02-19
  Changes: Database references