5JNE

E2-SUMO-Siz1 E3-SUMO-PCNA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Capturing a substrate in an activated RING E3/E2-SUMO complex.

Streich, F.C.Lima, C.D.

(2016) Nature 536: 304-308

  • DOI: 10.1038/nature19071
  • Primary Citation of Related Structures:  
    5JNE

  • PubMed Abstract: 
  • Post-translational protein modification by ubiquitin (Ub) and ubiquitin-like (Ubl) proteins such as small ubiquitin-like modifier (SUMO) regulates processes including protein homeostasis, the DNA damage response, and the cell cycle. Proliferating cel ...

    Post-translational protein modification by ubiquitin (Ub) and ubiquitin-like (Ubl) proteins such as small ubiquitin-like modifier (SUMO) regulates processes including protein homeostasis, the DNA damage response, and the cell cycle. Proliferating cell nuclear antigen (PCNA) is modified by Ub or poly-Ub at lysine (Lys)164 after DNA damage to recruit repair factors. Yeast PCNA is modified by SUMO on Lys164 and Lys127 during S-phase to recruit the anti-recombinogenic helicase Srs2. Lys164 modification requires specialized E2/E3 enzyme pairs for SUMO or Ub conjugation. For SUMO, Lys164 modification is strictly dependent on the E3 ligase Siz1, suggesting the E3 alters E2 specificity to promote Lys164 modification. The structural basis for substrate interactions in activated E3/E2–Ub/Ubl complexes remains unclear. Here we report an engineered E2 protein and cross-linking strategies that trap an E3/E2–Ubl/substrate complex for structure determination, illustrating how an E3 can bypass E2 specificity to force-feed a substrate lysine into the E2 active site.


    Organizational Affiliation

    Korea Nanobiotechnology Center, Pusan National University, Jangjeon-dong, Geumjeong-gu, Busan 609-735, Republic of Korea.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
E3 SUMO-protein ligase SIZ1,Ubiquitin-like protein SMT3AE367Saccharomyces cerevisiae S288CMutation(s): 1 
Gene Names: SIZ1ULL1YDR409W
EC: 6.3.2 (PDB Primary Data), 2.3.2 (UniProt)
Find proteins for Q12306 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12306 
Go to UniProtKB:  Q12306
Find proteins for Q04195 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q04195 
Go to UniProtKB:  Q04195
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
SUMO-conjugating enzyme UBC9BF160Saccharomyces cerevisiae S288CMutation(s): 3 
Gene Names: UBC9YDL064W
EC: 6.3.2 (PDB Primary Data), 2.3.2 (UniProt)
Find proteins for P50623 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P50623 
Go to UniProtKB:  P50623
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-like protein SMT3CG84Saccharomyces cerevisiae S288CMutation(s): 1 
Gene Names: SMT3YDR510WD9719.15
Find proteins for Q12306 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12306 
Go to UniProtKB:  Q12306
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Proliferating cell nuclear antigenDH258Saccharomyces cerevisiae S288CMutation(s): 5 
Gene Names: POL30YBR088CYBR0811
Find proteins for P15873 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P15873 
Go to UniProtKB:  P15873
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.421α = 90
b = 205.882β = 95.3
c = 142.501γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM065872

Revision History 

  • Version 1.0: 2016-08-10
    Type: Initial release
  • Version 1.1: 2016-08-24
    Changes: Database references
  • Version 1.2: 2016-08-31
    Changes: Database references
  • Version 1.3: 2016-09-21
    Changes: Other
  • Version 1.4: 2017-09-20
    Changes: Author supporting evidence, Derived calculations
  • Version 1.5: 2019-12-25
    Changes: Author supporting evidence