Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 18.26 kDa 
• Atom Count: 1386 
• Modelled Residue Count: 160 
• Deposited Residue Count: 160 
• Unique protein chains: 1

1U9A

HUMAN UBIQUITIN-CONJUGATING ENZYME UBC9

• PDB DOI: 10.2210/pdb1U9A/pdb

• Classification: UBIQUITIN-CONJUGATING ENZYME
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1997-02-11 Released: 1997-05-15 
• Deposition Author(s): Tong, H., Hateboer, G., Perrakis, A., Bernards, R., Sixma, T.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.250 
• R-Value Work: 0.160 

Literature

Crystal structure of murine/human Ubc9 provides insight into the variability of the ubiquitin-conjugating system.

Tong, H., Hateboer, G., Perrakis, A., Bernards, R., Sixma, T.K.

(1997) J Biol Chem 272: 21381-21387

• PubMed: 9261152 
• DOI: 10.1074/jbc.272.34.21381
• Primary Citation of Related Structures:  
  1U9A, 1U9B


• PubMed Abstract: 
  

Murine/human ubiquitin-conjugating enzyme Ubc9 is a functional homolog of Saccharomyces cerevisiae Ubc9 that is essential for the viability of yeast cells with a specific role in the G2-M transition of the cell cycle. The structure of recombinant mammalian Ubc9 has been determined from two crystal forms at 2.0 A resolution. Like Arabidopsis thaliana Ubc1 and S. cerevisiae Ubc4, murine/human Ubc9 was crystallized as a monomer, suggesting that previously reported hetero- and homo-interactions among Ubcs may be relatively weak or indirect. Compared with the known crystal structures of Ubc1 and Ubc4, which regulate different cellular processes, Ubc9 has a 5-residue insertion that forms a very exposed tight beta-hairpin and a 2-residue insertion that forms a bulge in a loop close to the active site. Mammalian Ubc9 also possesses a distinct electrostatic potential distribution that may provide possible clues to its remarkable ability to interact with other proteins. The 2-residue insertion and other sequence and structural heterogeneity observed at the catalytic site suggest that different Ubcs may utilize catalytic mechanisms of varying efficiency and substrate specificity.

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Organizational Affiliation: 

Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UBIQUITIN-CONJUGATING ENZYME	A	160	Mus musculus	Mutation(s): 0  Gene Names: Ube2i, Ubc9, Ubce2i, Ubce9 EC: 6.3.2.19 (PDB Primary Data), 2.3.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P63280 (Mus musculus) Explore P63280  Go to UniProtKB:  P63280
IMPC:  MGI:107365

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.250 
• R-Value Work: 0.160 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.04	α = 90
b = 35.18	β = 111.2
c = 58.1	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
TNT	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1997-02-11 
• Released Date: 1997-05-15 
Deposition Author(s): Tong, H., Hateboer, G., Perrakis, A., Bernards, R., Sixma, T.K.

Revision History  

• Version 1.0: 1997-05-15
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance