Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 25623.30 
• Atom Count: 1807 
• Residue Count: 226 
• Unique protein chains: 2

3A33

UbcH5b~Ubiquitin Conjugate

• DOI: 10.2210/pdb3A33/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2009-06-08 Released: 2009-11-24 
• Deposition Author(s): Sakata, E., Satoh, T., Yamamoto, S., Yamaguchi, Y., Yagi-Utsumi, M., Kurimoto, E., Wakatsuki, S., Kato, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.2 Å
• R-Value Free: 0.280 
• R-Value Work: 0.228 

Literature

Crystal Structure of UbcH5b~Ubiquitin Intermediate: Insight into the Formation of the Self-Assembled E2~Ub Conjugates

Sakata, E., Satoh, T., Yamamoto, S., Yamaguchi, Y., Yagi-Utsumi, M., Kurimoto, E., Tanaka, K., Wakatsuki, S., Kato, K.

(2010) Structure 18: 138-147

• PubMed: 20152160 
• DOI: 10.1016/j.str.2009.11.007


• PubMed Abstract: 
  

E2 ubiquitin-conjugating enzymes catalyze the attachment of ubiquitin to lysine residues of target proteins. The UbcH5b E2 enzyme has been shown to play a key role in the initiation of the ubiquitination of substrate proteins upon action of several E3 ligases. Here we have determined the 2.2 A crystal structure of an intermediate of UbcH5b~ubiquitin (Ub) conjugate, which is assembled into an infinite spiral through the backside interaction. This active complex may provide multiple E2 active sites, enabling efficient ubiquitination of substrates. Indeed, biochemical assays support a model in which the self-assembled UbcH5b~Ub can serve as a bridge for the gap between the lysine residue of the substrate and the catalytic cysteine of E2.

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Organizational Affiliation: 

Department of Structural Biology and Biomolecular Engineering, Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Ubiquitin-conjugating enzyme E2 D2	A	150	Homo sapiens	Mutation(s): 0  Gene Names: UBE2D2 (PUBC1, UBC4, UBC5B, UBCH4, UBCH5B) EC: 2.3.2.23
Find proteins for P62837 (Homo sapiens) Go to Gene View: UBE2D2 Go to UniProtKB:  P62837

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Ubiquitin	B	76	Homo sapiens	Mutation(s): 0  Gene Names: UBC
Find proteins for P0CG48 (Homo sapiens) Go to Gene View: UBC Go to UniProtKB:  P0CG48

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
GOL	A	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.2 Å
• R-Value Free: 0.280 
• R-Value Work: 0.228 
• Space Group: P 6₁ 2 2

Unit Cell:

Length (Å)	Angle (°)
a = 72.500	α = 90.00
b = 72.500	β = 90.00
c = 176.600	γ = 120.00

Software Package:

Software Name	Purpose
HKL-2000	data collection
DENZO	data reduction
REFMAC	refinement
MOLREP	phasing
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-06-08 
• Released Date: 2009-11-24 
• Deposition Author(s): Sakata, E., Satoh, T., Yamamoto, S., Yamaguchi, Y., Yagi-Utsumi, M., Kurimoto, E., Wakatsuki, S., Kato, K.

Revision History 

• Version 1.0: 2009-11-24
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Non-polymer description, Version format compliance