4I6J

A ubiquitin ligase-substrate complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

SCFFBXL3 ubiquitin ligase targets cryptochromes at their cofactor pocket.

Xing, W., Busino, L., Hinds, T.R., Marionni, S.T., Saifee, N.H., Bush, M.F., Pagano, M., Zheng, N.

(2013) Nature 496: 64-68

  • DOI: 10.1038/nature11964
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • The cryptochrome (CRY) flavoproteins act as blue-light receptors in plants and insects, but perform light-independent functions at the core of the mammalian circadian clock. To drive clock oscillations, mammalian CRYs associate with the Period protei ...

    The cryptochrome (CRY) flavoproteins act as blue-light receptors in plants and insects, but perform light-independent functions at the core of the mammalian circadian clock. To drive clock oscillations, mammalian CRYs associate with the Period proteins (PERs) and together inhibit the transcription of their own genes. The SCF(FBXL3) ubiquitin ligase complex controls this negative feedback loop by promoting CRY ubiquitination and degradation. However, the molecular mechanisms of their interactions and the functional role of flavin adenine dinucleotide (FAD) binding in CRYs remain poorly understood. Here we report crystal structures of mammalian CRY2 in its apo, FAD-bound and FBXL3-SKP1-complexed forms. Distinct from other cryptochromes of known structures, mammalian CRY2 binds FAD dynamically with an open cofactor pocket. Notably, the F-box protein FBXL3 captures CRY2 by simultaneously occupying its FAD-binding pocket with a conserved carboxy-terminal tail and burying its PER-binding interface. This novel F-box-protein-substrate bipartite interaction is susceptible to disruption by both FAD and PERs, suggesting a new avenue for pharmacological targeting of the complex and a multifaceted regulatory mechanism of CRY ubiquitination.

    Organizational Affiliation: 

    Department of Pharmacology, University of Washington, Seattle, Washington 98195, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cryptochrome-2
A
544Mus musculusMutation(s): 0 
Gene Names: Cry2 (Kiaa0658)
Find proteins for Q9R194 (Mus musculus)
Go to UniProtKB:  Q9R194
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
F-box/LRR-repeat protein 3
B
428Homo sapiensMutation(s): 0 
Gene Names: FBXL3 (FBL3A, FBXL3A)
Find proteins for Q9UKT7 (Homo sapiens)
Go to Gene View: FBXL3
Go to UniProtKB:  Q9UKT7
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
S-phase kinase-associated protein 1
C
163Homo sapiensMutation(s): 0 
Gene Names: SKP1 (EMC19, OCP2, SKP1A, TCEB1L)
Find proteins for P63208 (Homo sapiens)
Go to Gene View: SKP1
Go to UniProtKB:  P63208
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.203 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 125.389α = 90.00
b = 125.389β = 90.00
c = 145.712γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data collection
HKL-2000data scaling
PHENIXrefinement
PHENIXphasing
PHENIXmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-03-13
    Type: Initial release
  • Version 1.1: 2013-05-01
    Type: Database references