Crystal structure of HERC2 ZZ domain in complex with SUMO1 tail

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 

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This is version 1.3 of the entry. See complete history


Structural Insight into Binding of the ZZ Domain of HERC2 to Histone H3 and SUMO1.

Liu, J.Xue, Z.Zhang, Y.Vann, K.R.Shi, X.Kutateladze, T.G.

(2020) Structure 28: 1225-1230.e3

  • DOI: https://doi.org/10.1016/j.str.2020.07.003
  • Primary Citation of Related Structures:  
    6WW3, 6WW4

  • PubMed Abstract: 

    Human ubiquitin ligase HERC2, a component of the DNA repair machinery, has been linked to neurological diseases and cancer. Here, we show that the ZZ domain of HERC2 (HERC2 ZZ ) binds to histone H3 tail and tolerates posttranslational modifications commonly present in H3. The crystal structure of the HERC2 ZZ :H3 complex provides the molecular basis for this interaction and highlights a critical role of the negatively charged site of HERC2 ZZ in capturing of A1 of H3. NMR, mutagenesis, and fluorescence data reveal that HERC2 ZZ binds to H3 and the N-terminal tail of SUMO1, a previously reported ligand of HERC2 ZZ , with comparable affinities. Like H3, the N-terminal tail of SUMO1 occupies the same negatively charged site of HERC2 ZZ in the crystal structure of the complex, although in contrast to H3 it adopts an α-helical conformation. Our data suggest that HERC2 ZZ may play a role in mediating the association of HERC2 with chromatin.

  • Organizational Affiliation

    Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SUMO1 linked HERC2 ZZ domain (Small ubiquitin-related modifier 1,E3 ubiquitin-protein ligase HERC2)
A, B
60Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O95714 (Homo sapiens)
Explore O95714 
Go to UniProtKB:  O95714
PHAROS:  O95714
GTEx:  ENSG00000128731 
Find proteins for P63165 (Homo sapiens)
Explore P63165 
Go to UniProtKB:  P63165
PHAROS:  P63165
GTEx:  ENSG00000116030 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP63165O95714
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.882α = 90
b = 47.262β = 90
c = 55.476γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-05
    Type: Initial release
  • Version 1.1: 2020-08-12
    Changes: Database references
  • Version 1.2: 2020-11-11
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Advisory, Data collection, Database references, Refinement description