5IGO

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

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: 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 ...

    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. Electronic address: stephen_blacklow@hms.harvard.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase COP1ABCD336Arabidopsis thalianaMutation(s): 0 
Gene Names: COP1At2g32950T21L14.11
EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
Find proteins for P43254 (Arabidopsis thaliana)
Explore P43254 
Go to UniProtKB:  P43254
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Tribbles homolog 1UVWX8Homo sapiensMutation(s): 0 
Gene Names: TRIB1C8FWGIG2TRB1
Find proteins for Q96RU8 (Homo sapiens)
Explore Q96RU8 
Go to UniProtKB:  Q96RU8
NIH Common Fund Data Resources
PHAROS  Q96RU8
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 
  • Space Group: P 1 21 1
  • Diffraction Data DOI: 10.15785/SBGRID/264 SBGrid
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.516α = 90
b = 87.469β = 92.55
c = 94.61γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
Aimlessdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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