5IGQ

WD40 domain of Human E3 Ubiquitin Ligase COP1 (RFWD2) bound to peptide from Trib1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.9 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.228 

wwPDB Validation 3D Report Full Report


This is version 1.1 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:  

  • 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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
E3 ubiquitin-protein ligase RFWD2
A, B, C, D, E, F
353Homo sapiensGene Names: RFWD2 (COP1, RNF200)
EC: 2.3.2.27
Find proteins for Q8NHY2 (Homo sapiens)
Go to Gene View: RFWD2
Go to UniProtKB:  Q8NHY2
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Tribbles homolog 1
U
11Homo sapiensGene Names: TRIB1 (C8FW, GIG2, TRB1)
Find proteins for Q96RU8 (Homo sapiens)
Go to Gene View: TRIB1
Go to UniProtKB:  Q96RU8
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Tribbles homolog 1
V, W, X, Y, Z
8Homo sapiensGene Names: TRIB1 (C8FW, GIG2, TRB1)
Find proteins for Q96RU8 (Homo sapiens)
Go to Gene View: TRIB1
Go to UniProtKB:  Q96RU8
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.9 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.228 
  • Space Group: C 2 2 2
  • Diffraction Data DOI: 
    10.15785/SBGRID/265 SBGrid
Unit Cell:
Length (Å)Angle (°)
a = 247.646α = 90.00
b = 249.576β = 90.00
c = 124.512γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-04-20
    Type: Initial release
  • Version 1.1: 2016-05-11
    Type: Database references