3V7D

Crystal Structure of ScSkp1-ScCdc4-pSic1 peptide complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.197 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Composite low affinity interactions dictate recognition of the cyclin-dependent kinase inhibitor Sic1 by the SCFCdc4 ubiquitin ligase.

Tang, X.Orlicky, S.Mittag, T.Csizmok, V.Pawson, T.Forman-Kay, J.D.Sicheri, F.Tyers, M.

(2012) Proc Natl Acad Sci U S A 109: 3287-3292

  • DOI: https://doi.org/10.1073/pnas.1116455109
  • Primary Citation of Related Structures:  
    3V7D

  • PubMed Abstract: 

    The ubiquitin ligase SCF(Cdc4) (Skp1/Cul1/F-box protein) recognizes its substrate, the cyclin-dependent kinase inhibitor Sic1, in a multisite phosphorylation-dependent manner. Although short diphosphorylated peptides derived from Sic1 can bind to Cdc4 with high affinity, through systematic mutagenesis and quantitative biophysical analysis we show that individually weak, dispersed Sic1 phospho sites engage Cdc4 in a dynamic equilibrium. The affinities of individual phosphoepitopes serve to tune the overall phosphorylation site threshold needed for efficient recognition. Notably, phosphoepitope affinity for Cdc4 is dramatically weakened in the context of full-length Sic1, demonstrating the importance of regional environment on binding interactions. The multisite nature of the Sic1-Cdc4 interaction confers cooperative dependence on kinase activity for Sic1 recognition and ubiquitination under equilibrium reaction conditions. Composite dynamic interactions of low affinity sites may be a general mechanism to establish phosphorylation thresholds in biological responses.


  • Organizational Affiliation

    Center for Systems Biology, Samuel Lunenfeld Research Institute, Toronto, ON, Canada M5G 1X5.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Suppressor of kinetochore protein 1
A, C
169Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CBF3DD9798.14SKP1YDR328C
UniProt
Find proteins for P52286 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P52286 
Go to UniProtKB:  P52286
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP52286
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cell division control protein 4
B, D
464Saccharomyces cerevisiae S288CMutation(s): 2 
Gene Names: CDC4YFL009W
UniProt
Find proteins for P07834 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P07834 
Go to UniProtKB:  P07834
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07834
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Protein SIC119Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P38634 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38634 
Go to UniProtKB:  P38634
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38634
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
E
L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.197 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.292α = 90
b = 107.292β = 90
c = 166.679γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
ADSCdata collection

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-05-02
    Type: Initial release
  • Version 1.1: 2019-07-17
    Changes: Data collection, Derived calculations, Refinement description
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Refinement description