Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 8.36 kDa 
• Atom Count: 711 
• Modelled Residue Count: 72 
• Deposited Residue Count: 72 
• Unique protein chains: 1

1WM3

Crystal structure of human SUMO-2 protein

• DOI: 10.2210/pdb1WM3/pdb

• Classification: PROTEIN TRANSPORT
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2004-07-02 Released: 2004-11-30 
• Deposition Author(s): Huang, W.-C., Ko, T.-P., Li, S.S.-L., Wang, A.H.-J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 0.185 
• R-Value Work: 0.119 
• R-Value Observed: 0.122 

Literature

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

• PubMed: 15479240 
• DOI: 10.1111/j.1432-1033.2004.04349.x
• Primary Citation of Related Structures:  
  1WM3, 1WM2


• 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-like protein SMT3B	A	72	Homo sapiens	Mutation(s): 0  Gene Names: SUMO-2, SUMO2, SMT3B, SMT3H2
Find proteins for P61956 (Homo sapiens) Explore P61956  Go to UniProtKB:  P61956
NIH Common Fund Data Resources
PHAROS:  P61956 GTEx:  ENSG00000188612

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• 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 = 74.964	α = 90
b = 74.964	β = 90
c = 33.231	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-07-02 
• Released Date: 2004-11-30 
Deposition Author(s): Huang, W.-C., Ko, T.-P., Li, S.S.-L., Wang, A.H.-J.

Revision History  

• 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