4I6J

A ubiquitin ligase-substrate complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.206 

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:  
    4I6J, 4I6E, 4I6G

  • 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 proteins ( ...

    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
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cryptochrome-2 A544Mus musculusMutation(s): 0 
Gene Names: Cry2, Kiaa0658
Find proteins for Q9R194 (Mus musculus)
Explore Q9R194 
Go to UniProtKB:  Q9R194
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
F-box/LRR-repeat protein 3 B428Homo sapiensMutation(s): 0 
Gene Names: FBXL3, FBL3A, FBXL3A
Find proteins for Q9UKT7 (Homo sapiens)
Explore Q9UKT7 
Go to UniProtKB:  Q9UKT7
NIH Common Fund Data Resources
PHAROS:  Q9UKT7
GTEx:  ENSG00000005812
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
S-phase kinase-associated protein 1 C163Homo sapiensMutation(s): 0 
Gene Names: SKP1, EMC19, OCP2, SKP1A, TCEB1L
Find proteins for P63208 (Homo sapiens)
Explore P63208 
Go to UniProtKB:  P63208
NIH Common Fund Data Resources
PHAROS:  P63208
GTEx:  ENSG00000113558
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.206 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.389α = 90
b = 125.389β = 90
c = 145.712γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

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