Prediction of a common structural scaffold for proteasome lid, COP9-signalosome and eIF3 complexes

BMC Bioinformatics. 2005 Mar 24;6:71. doi: 10.1186/1471-2105-6-71.


Background: The 'lid' subcomplex of the 26S proteasome and the COP9 signalosome (CSN complex) share a common architecture consisting of six subunits harbouring a so-called PCI domain (proteasome, CSN, eIF3) at their C-terminus, plus two subunits containing MPN domains (Mpr1/Pad1 N-terminal). The translation initiation complex eIF3 also contains PCI- and MPN-domain proteins, but seems to deviate from the 6+2 stoichiometry. Initially, the PCI domain was defined as the region of detectable sequence similarity between the components mentioned above.

Results: During an exhaustive bioinformatical analysis of proteasome components, we detected multiple instances of tetratrico-peptide repeats (TPR) in the N-terminal region of most PCI proteins, suggesting that their homology is not restricted to the PCI domain. We also detected a previously unrecognized PCI domain in the eIF3 component eIF3k, a protein whose 3D-structure has been determined recently. By using profile-guided alignment techniques, we show that the structural elements found in eIF3k are most likely conserved in all PCI proteins, resulting in a structural model for the canonical PCI domain.

Conclusion: Our model predicts that the homology domain PCI is not a true domain in the structural sense but rather consists of two subdomains: a C-terminal 'winged helix' domain with a key role in PCI:PCI interaction, preceded by a helical repeat region. The TPR-like repeats detected in the N-terminal region of PCI proteins most likely form an uninterrupted extension of the repeats found within the PCI domain boundaries. This model allows an interpretation of several puzzling experimental results.

MeSH terms

  • Algorithms
  • Amino Acid Motifs
  • Amino Acid Sequence
  • Animals
  • COP9 Signalosome Complex
  • Computational Biology / methods*
  • Cysteine Endopeptidases / chemistry
  • Databases, Protein
  • Eukaryotic Initiation Factor-3 / chemistry*
  • Genome
  • Humans
  • Molecular Sequence Data
  • Multienzyme Complexes
  • Multiprotein Complexes / chemistry*
  • Peptide Hydrolases / chemistry*
  • Peptides / chemistry
  • Proteasome Endopeptidase Complex / chemistry*
  • Protein Structure, Tertiary
  • Sequence Homology, Amino Acid
  • Signal Transduction
  • Transcription Factors / chemistry
  • Ubiquitin / chemistry


  • Eukaryotic Initiation Factor-3
  • Multienzyme Complexes
  • Multiprotein Complexes
  • Peptides
  • Transcription Factors
  • Ubiquitin
  • Peptide Hydrolases
  • COP9 Signalosome Complex
  • Cysteine Endopeptidases
  • Proteasome Endopeptidase Complex