Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 40.63 kDa 
• Atom Count: 2725 
• Residue Count: 331 
• Unique protein chains: 2

3V61

Structure of S. cerevisiae PCNA conjugated to SUMO on lysine 164

• DOI: 10.2210/pdb3V61/pdb

• Classification: PROTEIN BINDING/DNA BINDING PROTEIN
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2011-12-18 Released: 2012-02-29 
• Deposition Author(s): Armstrong, A.A., Mohideen, F., Lima, C.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.254 
• R-Value Work: 0.214 
• R-Value Observed: 0.216 

Literature

Recognition of SUMO-modified PCNA requires tandem receptor motifs in Srs2.

Armstrong, A.A., Mohideen, F., Lima, C.D.

(2012) Nature 483: 59-63

• PubMed: 22382979 
• DOI: 10.1038/nature10883
• Primary Citation of Related Structures:  
  3V60, 3V61, 3V62


• PubMed Abstract: 
  

Ubiquitin (Ub) and ubiquitin-like (Ubl) modifiers such as SUMO (also known as Smt3 in Saccharomyces cerevisiae) mediate signal transduction through post-translational modification of substrate proteins in pathways that control differentiation, apoptosis and the cell cycle, and responses to stress such as the DNA damage response. In yeast, the proliferating cell nuclear antigen PCNA (also known as Pol30) is modified by ubiquitin in response to DNA damage and by SUMO during S phase. Whereas Ub-PCNA can signal for recruitment of translesion DNA polymerases, SUMO-PCNA signals for recruitment of the anti-recombinogenic DNA helicase Srs2. It remains unclear how receptors such as Srs2 specifically recognize substrates after conjugation to Ub and Ubls. Here we show, through structural, biochemical and functional studies, that the Srs2 carboxy-terminal domain harbours tandem receptor motifs that interact independently with PCNA and SUMO and that both motifs are required to recognize SUMO-PCNA specifically. The mechanism presented is pertinent to understanding how other receptors specifically recognize Ub- and Ubl-modified substrates to facilitate signal transduction.

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Organizational Affiliation: 

Structural Biology Program, Sloan-Kettering Institute, New York, New York 10065, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-like protein SMT3	A	84	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: D9719.15, SMT3, YDR510W
Find proteins for Q12306 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12306  Go to UniProtKB:  Q12306

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Proliferating cell nuclear antigen	B	258	Saccharomyces cerevisiae S288C	Mutation(s): 1  Gene Names: POL30, YBR0811, YBR088C
Find proteins for P15873 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P15873  Go to UniProtKB:  P15873

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BA	A, B	BARIUM ION Ba XDFCIPNJCBUZJN-UHFFFAOYSA-N
NEQ	B	N-ETHYLMALEIMIDE C6 H7 N O2 HDFGOPSGAURCEO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.254 
• R-Value Work: 0.214 
• R-Value Observed: 0.216 
• Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 140.06	α = 90
b = 140.06	β = 90
c = 52.119	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-12-18 
• Released Date: 2012-02-29 
Deposition Author(s): Armstrong, A.A., Mohideen, F., Lima, C.D.

Revision History 

• Version 1.0: 2012-02-29
  Type: Initial release
  
• Version 1.1: 2013-04-03
  Changes: Database references
• Version 1.2: 2013-09-18
  Changes: Other
• Version 1.3: 2017-10-25
  Changes: Author supporting evidence, Refinement description