Biological Assembly 1  

 3D View: Structure

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 5.74 kDa 
• Atom Count: 403 
• Residue Count: 52 
• Unique protein chains: 1

2JY7

NMR structure of the ubiquitin associated (UBA) domain of p62 (SQSTM1). RDC refined

• DOI: 10.2210/pdb2JY7/pdb
• BMRB: 15591

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-12-07 Released: 2007-12-18 
• Deposition Author(s): Long, J.E., Layfield, R., Searle, M.S.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 30 
• Selection Criteria: structures with the lowest energy 

Literature

Ubiquitin Recognition by the Ubiquitin-associated Domain of p62 Involves a Novel Conformational Switch

Long, J., Gallagher, T.R., Cavey, J.R., Sheppard, P.W., Ralston, S.H., Layfield, R., Searle, M.S.

(2008) J Biol Chem 283: 5427-5440

• PubMed: 18083707 
• DOI: 10.1074/jbc.M704973200
• Primary Citation of Related Structures:  
  2JY8, 2JY7


• PubMed Abstract: 
  

The p62 protein functions as a scaffold in signaling pathways that lead to activation of NF-kappaB and is an important regulator of osteoclastogenesis. Mutations affecting the receptor activator of NF-kappaB signaling axis can result in human skeletal disorders, including those identified in the C-terminal ubiquitin-associated (UBA) domain of p62 in patients with Paget disease of bone. These observations suggest that the disease may involve a common mechanism related to alterations in the ubiquitin-binding properties of p62. The structural basis for ubiquitin recognition by the UBA domain of p62 has been investigated using NMR and reveals a novel binding mechanism involving a slow exchange structural reorganization of the UBA domain to a "bound" non-canonical UBA conformation that is not significantly populated in the absence of ubiquitin. The repacking of the three-helix bundle generates a binding surface localized around the conserved Xaa-Gly-Phe-Xaa loop that appears to optimize both hydrophobic and electrostatic surface complementarity with ubiquitin. NMR titration analysis shows that the p62-UBA binds to Lys 48-linked di-ubiquitin with approximately 4-fold lower affinity than to mono-ubiquitin, suggesting preferential binding of the p62-UBA to single ubiquitin units, consistent with the apparent in vivo preference of the p62 protein for Lys 63-linked polyubiquitin chains (which adopt a more open and extended structure). The conformational switch observed on binding may represent a novel mechanism that underlies specificity in regulating signalinduced protein recognition events.

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Organizational Affiliation: 

School of Chemistry, Centre for Biomolecular Sciences, University of Nottingham, Nottingham NG7 2RD, United Kingdom.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-binding protein p62	A	52	Homo sapiens	Mutation(s): 0  Gene Names: SQSTM1, ORCA, OSIL
Find proteins for Q13501 (Homo sapiens) Explore Q13501  Go to UniProtKB:  Q13501
NIH Common Fund Data Resources
PHAROS:  Q13501 GTEx:  ENSG00000161011

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 30 
• Selection Criteria: structures with the lowest energy 
• OLDERADO: 2JY7 Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-12-07 
• Released Date: 2007-12-18 
Deposition Author(s): Long, J.E., Layfield, R., Searle, M.S.

Revision History 

• Version 1.0: 2007-12-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2020-02-19
  Changes: Data collection, Database references, Derived calculations, Other