Biological Assembly 1  

 3D View: Structure | Electron Density

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - AB Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Homo 2-mer -A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 35048.19 
• Atom Count: 2351 
• Residue Count: 313 
• Unique protein chains: 2

4ONL

Crystal structure of human Mms2/Ubc13_D81N, R85S, A122V, N123P

• DOI: 10.2210/pdb4ONL/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): 3 


• Deposited: 2014-01-28 Released: 2015-05-06 
• Deposition Author(s): Hodge, C.D., Edwards, R.A., Glover, J.N.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 0.199 
• R-Value Work: 0.171 

Literature

Covalent Inhibition of Ubc13 Affects Ubiquitin Signaling and Reveals Active Site Elements Important for Targeting.

Hodge, C.D., Edwards, R.A., Markin, C.J., McDonald, D., Pulvino, M., Huen, M.S., Zhao, J., Spyracopoulos, L., Hendzel, M.J., Glover, J.N.

(2015) Acs Chem.Biol. 10: 1718-1728

• PubMed: 25909880 
• DOI: 10.1021/acschembio.5b00222
• Primary Citation of Related Structures:  
  4ONN, 4ONM


• PubMed Abstract: 
  

Ubc13 is an E2 ubiquitin conjugating enzyme that functions in nuclear DNA damage signaling and cytoplasmic NF-κB signaling. Here, we present the structures of complexes of Ubc13 with two inhibitors, NSC697923 and BAY 11-7082, which inhibit DNA damage and NF-κB signaling in human cells. NSC697923 and BAY 11-7082 both inhibit Ubc13 by covalent adduct formation through a Michael addition at the Ubc13 active site cysteine. The resulting adducts of both compounds exploit a binding groove unique to Ubc13. We developed a Ubc13 mutant which resists NSC697923 inhibition and, using this mutant, we show that the inhibition of cellular DNA damage and NF-κB signaling by NSC697923 is largely due to specific Ubc13 inhibition. We propose that unique structural features near the Ubc13 active site could provide a basis for the rational development and design of specific Ubc13 inhibitors.

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Organizational Affiliation: 

†Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2H7.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Ubiquitin-conjugating enzyme E2 variant 2	A	153	Homo sapiens	Mutation(s): 0  Gene Names: UBE2V2 (MMS2, UEV2)
Find proteins for Q15819 (Homo sapiens) Go to Gene View: UBE2V2 Go to UniProtKB:  Q15819

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Ubiquitin-conjugating enzyme E2 N	B	160	Homo sapiens	Mutation(s): 3  Gene Names: UBE2N (BLU) EC: 2.3.2.23
Find proteins for P61088 (Homo sapiens) Go to Gene View: UBE2N Go to UniProtKB:  P61088

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 0.199 
• R-Value Work: 0.171 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 43.933	α = 90.00
b = 74.942	β = 90.00
c = 92.055	γ = 90.00

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-01-28 
• Released Date: 2015-05-06 
• Deposition Author(s): Hodge, C.D., Edwards, R.A., Glover, J.N.M.

Revision History 

• Version 1.0: 2015-05-06
  Type: Initial release
• Version 1.1: 2015-08-05
  Type: Database references