3V61

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


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 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


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

  • DOI: https://doi.org/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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-like protein SMT384Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: D9719.15SMT3YDR510W
UniProt
Find proteins for Q12306 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12306 
Go to UniProtKB:  Q12306
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12306
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Proliferating cell nuclear antigen258Saccharomyces cerevisiae S288CMutation(s): 1 
Gene Names: POL30YBR0811YBR088C
UniProt
Find proteins for P15873 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P15873 
Go to UniProtKB:  P15873
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15873
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BA
Query on BA

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth B]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth B],
H [auth B],
I [auth B],
J [auth B],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
O [auth B]
BARIUM ION
Ba
XDFCIPNJCBUZJN-UHFFFAOYSA-N
NEQ
Query on NEQ

Download Ideal Coordinates CCD File 
P [auth B],
Q [auth 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 = 140.06α = 90
b = 140.06β = 90
c = 52.119γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.4: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description