Biological Assembly 1  

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

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 14.21 kDa 
• Atom Count: 998 
• Modelled Residue Count: 128 
• Deposited Residue Count: 128 
• Unique protein chains: 2

2JY6

Solution structure of the complex of ubiquitin and ubiquilin 1 UBA domain

• PDB DOI: 10.2210/pdb2JY6/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2007-12-06 Released: 2008-03-18 
• Deposition Author(s): Zhang, D., Raasi, S., Fushman, D.

---

Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 500 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Literature

Affinity makes the difference: nonselective interaction of the UBA domain of Ubiquilin-1 with monomeric ubiquitin and polyubiquitin chains

Zhang, D., Raasi, S., Fushman, D.

(2008) J Mol Biol 377: 162-180

• PubMed: 18241885 
• DOI: 10.1016/j.jmb.2007.12.029
• Primary Citation of Related Structures:  
  2JY5, 2JY6


• PubMed Abstract: 
  

Ubiquilin/PLIC proteins belong to the family of UBL-UBA proteins implicated in the regulation of the ubiquitin-dependent proteasomal degradation of cellular proteins. A human presenilin-interacting protein, ubiquilin-1, has been suggested as potential therapeutic target for treating Huntington's disease. Ubiquilin's interactions with mono- and polyubiquitins are mediated by its UBA domain, which is one of the tightest ubiquitin binders among known ubiquitin-binding domains. Here we report the three-dimensional structure of the UBA domain of ubiquilin-1 (UQ1-UBA) free in solution and in complex with ubiquitin. UQ1-UBA forms a compact three-helix bundle structurally similar to other known UBAs, and binds to the hydrophobic patch on ubiquitin with a K(d) of 20 microM. To gain structural insights into UQ1-UBA's interactions with polyubiquitin chains, we have mapped the binding interface between UQ1-UBA and Lys48- and Lys63-linked di-ubiquitins and characterized the strength of UQ1-UBA binding to these chains. Our NMR data show that UQ1-UBA interacts with the individual ubiquitin units in both chains in a mode similar to its interaction with mono-ubiquitin, although with an improved binding affinity for the chains. Our results indicate that, in contrast to UBA2 of hHR23A that has strong binding preference for Lys48-linked chains, UQ1-UBA shows little or no binding selectivity toward a particular chain linkage or between the two ubiquitin moieties in the same chain. The structural data obtained in this study provide insights into the possible structural reasons for the diversity of polyubiquitin chain recognition by UBA domains.

---

Organizational Affiliation: 

Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20910, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin protein	A	76	Homo sapiens	Mutation(s): 0  Gene Names: UBI1, RPL40A, UBC
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG48 (Homo sapiens) Explore P0CG48  Go to UniProtKB:  P0CG48
PHAROS:  P0CG48

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquilin-1	B	52	Homo sapiens	Mutation(s): 0  Gene Names: UBQLN1, DA41, PLIC1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UMX0 (Homo sapiens) Explore Q9UMX0  Go to UniProtKB:  Q9UMX0
PHAROS:  Q9UMX0 GTEx:  ENSG00000135018

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 500 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 
• OLDERADO: 2JY6 Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-12-06 
• Released Date: 2008-03-18 
Deposition Author(s): Zhang, D., Raasi, S., Fushman, D.

Revision History  

• Version 1.0: 2008-03-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2022-03-16
  Changes: Data collection, Database references, Derived calculations