4MJS

crystal structure of a PB1 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.240 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural and biochemical insights into the homotypic PB1-PB1 complex between PKC zeta and p62

Ren, J.Wang, J.Wang, Z.X.Wu, J.W.

(2014) Sci China Life Sci 57: 69-80

  • DOI: https://doi.org/10.1007/s11427-013-4592-z
  • Primary Citation of Related Structures:  
    4MJS

  • PubMed Abstract: 

    The atypical PKC isoforms (ζ and ı) play essential roles in regulating various cellular processes. Both the hetero-interaction between PKCζ and p62 through their N-terminal PB1 domains and the homo-oligomerization of p62 via its PB1 domain are critical for the activation of NF-κB signaling; however, the molecular mechanisms concerning the formation and regulation of these homotypic complexes remain unclear. Here we determined the crystal structure of PKCζ-PB1 in complex with a monomeric p62-PB1 mutant, where the massive electrostatic interactions between the acidic OPCA motif of PKCζ-PB1 and the basic surface of p62-PB1, as well as additional hydrogen bonds, ensure the formation of a stable and specific complex. The PKCζ-p62 interaction is interfered with the modification of a specific Cys of PKCζ by the antiarthritis drug aurothiomalate, though all four cysteine residues in the PKCζ-PB1 domain can be modified in in vitro assay. In addition, detailed structural and biochemical analyses demonstrate that the PB1 domains of aPKCs belong to the type I group, which can depolymerize the high-molecular-weight p62 aggregates into homo-oligomers of lower order. These data together unravel the molecular mechanisms of the homo-or hetero-interactions between p62 and PKCζ and provide the basis for designing inhibitors of NF-κB signaling.


  • Organizational Affiliation

    MOE Key Laboratory of Protein Science and Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein kinase C zeta type
A, C, E, G, I
A, C, E, G, I, K, M, O, Q, S, U, W
91Rattus norvegicusMutation(s): 0 
Gene Names: PkczPrkcz
EC: 2.7.11.13
UniProt
Find proteins for P09217 (Rattus norvegicus)
Explore P09217 
Go to UniProtKB:  P09217
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09217
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Sequestosome-1
B, D, F, H, J
B, D, F, H, J, L, N, P, R, T, V, X
104Homo sapiensMutation(s): 2 
Gene Names: ORCAOSILSQSTM1
UniProt & NIH Common Fund Data Resources
Find proteins for Q13501 (Homo sapiens)
Explore Q13501 
Go to UniProtKB:  Q13501
PHAROS:  Q13501
GTEx:  ENSG00000161011 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13501
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.240 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.715α = 90
b = 135.681β = 90
c = 259.559γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
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: 2014-08-27
    Type: Initial release
  • Version 1.1: 2014-10-29
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description