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: 25451.09 
• Atom Count: 1779 
• Residue Count: 223 
• Unique protein chains: 2

3UGB

UbcH5c~Ubiquitin Conjugate

• DOI: 10.2210/pdb3UGB/pdb

• Classification: LIGASE/PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): 1 


• Deposited: 2011-11-02 Released: 2012-05-16 
• Deposition Author(s): Page, R.C., Pruneda, J.N., Klevit, R.E., Misra, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.252 
• R-Value Work: 0.211 

Literature

Structural insights into the conformation and oligomerization of E2~ubiquitin conjugates.

Page, R.C., Pruneda, J.N., Amick, J., Klevit, R.E., Misra, S.

(2012) Biochemistry 51: 4175-4187

• PubMed: 22551455 
• DOI: 10.1021/bi300058m


• PubMed Abstract: 
  

Post-translational modification of proteins by ubiquitin (Ub) regulates a host of cellular processes, including protein quality control, DNA repair, endocytosis, and cellular signaling. In the ubiquitination cascade, a thioester-linked conjugate between the C-terminus of Ub and the active site cysteine of a ubiquitin-conjugating enzyme (E2) is formed. The E2~Ub conjugate interacts with a ubiquitin ligase (E3) to transfer Ub to a lysine residue on a target protein. The flexibly linked E2~Ub conjugates have been shown to form a range of structures in solution. In addition, select E2~Ub conjugates oligomerize through a noncovalent "backside" interaction between Ub and E2 components of different conjugates. Additional studies are needed to bridge the gap between the dynamic monomeric conjugates, E2~Ub oligomers, and the mechanisms of ubiquitination. We present a new 2.35 Å crystal structure of an oligomeric UbcH5c~Ub conjugate. The conjugate forms a staggered linear oligomer that differs substantially from the "infinite spiral" helical arrangement of the only previously reported structure of an oligomeric conjugate. Our structure also differs in intraconjugate conformation from other structurally characterized conjugates. Despite these differences, we find that the backside interaction mode is conserved in different conjugate oligomers and is independent of intraconjugate relative E2-Ub orientations. We delineate a common intraconjugate E2-binding surface on Ub. In addition, we demonstrate that an E3 CHIP (carboxyl terminus of Hsp70 interacting protein) interacts directly with UbcH5c~Ub oligomers, not only with conjugate monomers. These results provide insights into the conformational diversity of E2~Ub conjugates and conjugate oligomers, and into their compatibility and interactions with E3s, which have important consequences for the ubiquitination process.

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Organizational Affiliation: 

Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, USA. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Ubiquitin-conjugating enzyme E2 D3	A	147	Homo sapiens	Mutation(s): 1  Gene Names: UBE2D3 (UBC5C, UBCH5C) EC: 2.3.2.23
Find proteins for P61077 (Homo sapiens) Go to Gene View: UBE2D3 Go to UniProtKB:  P61077

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Polyubiquitin-C	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: 2.35 Å
• R-Value Free: 0.252 
• R-Value Work: 0.211 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 42.027	α = 90.00
b = 52.510	β = 101.07
c = 53.114	γ = 90.00

Software Package:

Software Name	Purpose
d*TREK	data scaling
PHENIX	model building
StructureStudio	data collection
PHENIX	refinement
PHENIX	phasing
d*TREK	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-11-02 
• Released Date: 2012-05-16 
• Deposition Author(s): Page, R.C., Pruneda, J.N., Klevit, R.E., Misra, S.

Revision History 

• Version 1.0: 2012-05-16
  Type: Initial release
• Version 1.1: 2012-11-14
  Type: Database references