p62/SQSTM1 ZZ domain with Gly-peptide

Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.240 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Use of the LC3B-fusion technique for biochemical and structural studies of proteins involved in the N-degron pathway.

Kim, L.Kwon, D.H.Heo, J.Park, M.R.Song, H.K.

(2020) J Biol Chem 295: 2590-2600

  • DOI: https://doi.org/10.1074/jbc.RA119.010912
  • Primary Citation of Related Structures:  
    6KGI, 6KGJ, 6KHZ, 6LHN

  • PubMed Abstract: 

    The N-degron pathway, formerly the N-end rule pathway, is a protein degradation process that determines the half-life of proteins based on their N-terminal residues. In contrast to the well-established in vivo studies over decades, in vitro studies of this pathway, including biochemical characterization and high-resolution structures, are relatively limited. In this study, we have developed a unique fusion technique using microtubule-associated protein 1A/1B light chain 3B, a key marker protein of autophagy, to tag the N terminus of the proteins involved in the N-degron pathway, which enables high yield of homogeneous target proteins with variable N-terminal residues for diverse biochemical studies including enzymatic and binding assays and substrate identification. Intriguingly, crystallization showed a markedly enhanced probability, even for the N-degron complexes. To validate our results, we determined the structures of select proteins in the N-degron pathway and compared them with the Protein Data Bank-deposited proteins. Furthermore, several biochemical applications of this technique were introduced. Therefore, this technique can be used as a general tool for the in vitro study of the N-degron pathway.

  • Organizational Affiliation

    Department of Life Sciences, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, South Korea.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D
50Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q13501 (Homo sapiens)
Explore Q13501 
Go to UniProtKB:  Q13501
GTEx:  ENSG00000161011 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13501
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.240 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.979α = 90
b = 113.979β = 90
c = 113.979γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-22
    Type: Initial release
  • Version 1.1: 2020-03-11
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description