WD40 domain of Arabidopsis thaliana E3 Ubiquitin Ligase COP1 in complex with peptide from Trib1

Experimental Data Snapshot

  • Resolution: 1.60 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 

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This is version 1.4 of the entry. See complete history


Structural Basis for Substrate Selectivity of the E3 Ligase COP1.

Uljon, S.Xu, X.Durzynska, I.Stein, S.Adelmant, G.Marto, J.A.Pear, W.S.Blacklow, S.C.

(2016) Structure 24: 687-696

  • DOI: https://doi.org/10.1016/j.str.2016.03.002
  • Primary Citation of Related Structures:  
    5HQG, 5IGO, 5IGQ

  • PubMed Abstract: 

    COP1 proteins are E3 ubiquitin ligases that regulate phototropism in plants and target transcription factors for degradation in mammals. The substrate-binding region of COP1 resides within a WD40-repeat domain that also binds to Trib proteins, which are adaptors for C/EBPα degradation. Here we report structures of the human COP1 WD40 domain in isolation, and complexes of the human and Arabidopsis thaliana COP1 WD40 domains with the binding motif of Trib1. The human and Arabidopsis WD40 domains are seven-bladed β propellers with an inserted loop on the bottom face of the first blade. The Trib1 peptide binds in an extended conformation to a highly conserved surface on the top face of the β propeller, indicating a general mode for recognition of peptide motifs by COP1. Together, these studies identify the structural basis and key interactions for motif recognition by COP1, and hint at how Trib1 autoinhibition is overcome to target C/EBPα for degradation.

  • Organizational Affiliation

    Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase COP1A,
C [auth B],
E [auth C],
G [auth D]
336Arabidopsis thalianaMutation(s): 0 
Gene Names: COP1At2g32950T21L14.11
EC: 6.3.2
Find proteins for P43254 (Arabidopsis thaliana)
Explore P43254 
Go to UniProtKB:  P43254
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43254
Sequence Annotations
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Tribbles homolog 1B [auth U],
D [auth V],
F [auth W],
H [auth X]
8Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q96RU8 (Homo sapiens)
Explore Q96RU8 
Go to UniProtKB:  Q96RU8
GTEx:  ENSG00000173334 
Entity Groups  
UniProt GroupQ96RU8
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.516α = 90
b = 87.469β = 92.55
c = 94.61γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
Aimlessdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-04-20
    Type: Initial release
  • Version 1.1: 2016-05-11
    Changes: Database references
  • Version 1.2: 2016-07-20
    Changes: Data collection
  • Version 1.3: 2017-11-22
    Changes: Derived calculations, Refinement description
  • Version 1.4: 2023-09-27
    Changes: Data collection, Database references, Refinement description