Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

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

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

Macromolecule Content

• Total Structure Weight: 42.03 kDa 
• Atom Count: 2647 
• Modelled Residue Count: 335 
• Deposited Residue Count: 371 
• Unique protein chains: 2

3PGE

Structure of sumoylated PCNA

• PDB DOI: 10.2210/pdb3PGE/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-11-01 Released: 2010-12-29 
• Deposition Author(s): Freudenthal, B.D., Brogie, J.E., Gakhar, L., Washington, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.253 
• R-Value Work: 0.231 
• R-Value Observed: 0.232 

Literature

Crystal Structure of SUMO-Modified Proliferating Cell Nuclear Antigen.

Freudenthal, B.D., Brogie, J.E., Gakhar, L., Kondratick, C.M., Washington, M.T.

(2011) J Mol Biol 406: 9-17

• PubMed: 21167178 
• DOI: 10.1016/j.jmb.2010.12.015
• Primary Citation of Related Structures:  
  3PGE


• PubMed Abstract: 
  

Eukaryotic proliferating cell nuclear antigen (PCNA) is a replication accessory protein that functions in DNA replication, repair, and recombination. The various functions of PCNA are regulated by posttranslational modifications including mono-ubiquitylation, which promotes translesion synthesis, and sumoylation, which inhibits recombination. To understand how SUMO modification regulates PCNA, we generated a split SUMO-modified PCNA protein and showed that it supports cell viability and stimulates DNA polymerase δ activity. We then determined its X-ray crystal structure and found that SUMO occupies a position on the back face of the PCNA ring, which is distinct from the position occupied by ubiquitin in the structure of ubiquitin-modified PCNA. We propose that the back of PCNA has evolved to be a site of regulation that can be easily modified without disrupting ongoing reactions on the front of PCNA, such as normal DNA replication. Moreover, these modifications likely allow PCNA to function as a tool belt, whereby proteins can be recruited to the replication machinery via the back of PCNA and be held in reserve until needed.

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Organizational Affiliation: 

Department of Biochemistry, University of Iowa College of Medicine, Iowa City, IA 52242-1109, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SUMO-modified proliferating cell nuclear antigen	A	200	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for Q12306 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12306  Go to UniProtKB:  Q12306
Find proteins for P15873 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P15873  Go to UniProtKB:  P15873
UniProt Groups	P15873Q12306

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Proliferating cell nuclear antigen	B	171	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P15873 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P15873  Go to UniProtKB:  P15873

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.253 
• R-Value Work: 0.231 
• R-Value Observed: 0.232 
• Space Group: F 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 268.816	α = 90
b = 268.816	β = 90
c = 268.816	γ = 90

Software Package:

Software Name	Purpose
StructureStudio	data collection
PHASER	phasing
PHENIX	refinement
d*TREK	data reduction
d*TREK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-11-01 
• Released Date: 2010-12-29 
Deposition Author(s): Freudenthal, B.D., Brogie, J.E., Gakhar, L., Washington, T.

Revision History  

• Version 1.0: 2010-12-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-08-02
  Changes: Refinement description, Source and taxonomy