2OXQ

Structure of the UbcH5 :CHIP U-box complex

• PDB DOI: https://doi.org/10.2210/pdb2OXQ/pdb

• Classification: LIGASE
• Organism(s): Danio rerio
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-02-20 Released: 2008-02-19 
• Deposition Author(s): Xu, Z., Nix, J.C., Devlin, K.I., Misra, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.272 
• R-Value Work: 0.240 

Literature

Interactions between the quality control ubiquitin ligase CHIP and ubiquitin conjugating enzymes.

Xu, Z., Kohli, E., Devlin, K.I., Bold, M., Nix, J.C., Misra, S.

(2008) BMC Struct Biol 8: 26-26

• PubMed: 18485199 
• DOI: https://doi.org/10.1186/1472-6807-8-26
• Primary Citation of Related Structures:  
  2OXQ


• PubMed Abstract: 
  

  Ubiquitin (E3) ligases interact with specific ubiquitin conjugating (E2) enzymes to ubiquitinate particular substrate proteins. As the combination of E2 and E3 dictates the type and biological consequence of ubiquitination, it is important to understand the basis of specificity in E2:E3 interactions. The E3 ligase CHIP interacts with Hsp70 and Hsp90 and ubiquitinates client proteins that are chaperoned by these heat shock proteins. CHIP interacts with two types of E2 enzymes, UbcH5 and Ubc13-Uev1a. It is unclear, however, why CHIP binds these E2 enzymes rather than others, and whether CHIP interacts preferentially with UbcH5 or Ubc13-Uev1a, which form different types of polyubiquitin chains.

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Organizational Affiliation: 

Department of Molecular Cardiology, Lerner Research Institute, The Cleveland Clinic, Cleveland, Ohio, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 52.34 kDa 
• Atom Count: 3,525 
• Modelled Residue Count: 442 
• Deposited Residue Count: 464 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-conjugating enzyme E2D 1	A, B	152	Danio rerio	Mutation(s): 0  Gene Names: ube2d1 EC: 6.3.2.19
UniProt
Find proteins for Q6PC58 (Danio rerio) Explore Q6PC58  Go to UniProtKB:  Q6PC58

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
STIP1 homology and U-Box containing protein 1	C, D	80	Danio rerio	Mutation(s): 0  Gene Names: stub1
UniProt
Find proteins for F6NGW2 (Danio rerio) Explore F6NGW2  Go to UniProtKB:  F6NGW2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	E [auth C], F [auth D], G [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.272 
• R-Value Work: 0.240 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.042	α = 90
b = 93.399	β = 90
c = 144.009	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data scaling
CNS	refinement
d*TREK	data reduction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-02-19 
Deposition Author(s): Xu, Z., Nix, J.C., Devlin, K.I., Misra, S.

Revision History  

• Version 1.0: 2008-02-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description