Crystal structure of human SUMO-2 protein

Experimental Data Snapshot

  • Resolution: 1.20 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.119 
  • R-Value Observed: 0.122 

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This is version 1.3 of the entry. See complete history


Crystal structures of the human SUMO-2 protein at 1.6 A and 1.2 A resolution: implication on the functional differences of SUMO proteins

Huang, W.-C.Ko, T.-P.Li, S.S.-L.Wang, A.H.-J.

(2004) Eur J Biochem 271: 4114-4122

  • DOI: https://doi.org/10.1111/j.1432-1033.2004.04349.x
  • Primary Citation of Related Structures:  
    1WM2, 1WM3

  • PubMed Abstract: 

    The SUMO proteins are a class of small ubiquitin-like modifiers. SUMO is attached to a specific lysine side chain on the target protein via an isopeptide bond with its C-terminal glycine. There are at least four SUMO proteins in humans, which are involved in protein trafficking and targeting. A truncated human SUMO-2 protein that contains residues 9-93 was expressed in Escherichia coli and crystallized in two different unit cells, with dimensions of a=b=75.25 A, c=29.17 A and a=b=74.96 A, c=33.23 A, both belonging to the rhombohedral space group R3. They diffracted X-rays to 1.6 A and 1.2 A resolution, respectively. The structures were determined by molecular replacement using the yeast SMT3 protein as a search model. Subsequent refinements yielded R/Rfree values of 0.169/0.190 and 0.119/0.185, at 1.6 A and 1.2 A, respectively. The peptide folding of SUMO-2 consists of a half-open beta-barrel and two flanking alpha-helices with secondary structural elements arranged as betabetaalphabetabetaalphabeta in the sequence, identical to those of ubiquitin, SMT3 and SUMO-1. Comparison of SUMO-2 with SUMO-1 showed a surface region near the C terminus with significantly different charge distributions. This may explain their distinct intracellular locations. In addition, crystal-packing analysis suggests a possible trimeric assembly of the SUMO-2 protein, of which the biological significance remains to be determined.

  • Organizational Affiliation

    Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-like protein SMT3B72Homo sapiensMutation(s): 0 
Gene Names: SUMO-2
UniProt & NIH Common Fund Data Resources
Find proteins for P61956 (Homo sapiens)
Explore P61956 
Go to UniProtKB:  P61956
GTEx:  ENSG00000188612 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61956
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.20 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.119 
  • R-Value Observed: 0.122 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.964α = 90
b = 74.964β = 90
c = 33.231γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-11-30
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-10-25
    Changes: Data collection, Database references, Refinement description