4GGD

Structural analysis of human Cdc20 supports multisite degron recognition by APC/C.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.157 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history. 


Literature

Structural analysis of human Cdc20 supports multisite degron recognition by APC/C.

Tian, W., Li, B., Warrington, R., Tomchick, D.R., Yu, H., Luo, X.

(2012) Proc Natl Acad Sci U S A 109: 18419-18424

  • DOI: 10.1073/pnas.1213438109
  • Primary Citation of Related Structures:  
    4GGA, 4GGC, 4GGD

  • PubMed Abstract: 

    • The anaphase-promoting complex/cyclosome (APC/C) promotes anaphase onset and mitotic exit through ubiquitinating securin and cyclin B1. The mitotic APC/C activator, the cell division cycle 20 (Cdc20) protein, directly interacts with APC/C degrons--the destruction (D) and KEN boxes ...

    The anaphase-promoting complex/cyclosome (APC/C) promotes anaphase onset and mitotic exit through ubiquitinating securin and cyclin B1. The mitotic APC/C activator, the cell division cycle 20 (Cdc20) protein, directly interacts with APC/C degrons--the destruction (D) and KEN boxes. APC/C(Cdc20) is the target of the spindle checkpoint. Checkpoint inhibition of APC/C(Cdc20) requires the binding of a BubR1 KEN box to Cdc20. How APC/C recognizes substrates is not understood. We report the crystal structures of human Cdc20 alone or bound to a BubR1 KEN box. Cdc20 has a disordered N-terminal region and a C-terminal WD40 β propeller with a preformed KEN-box-binding site at its top face. We identify a second conserved surface at the side of the Cdc20 β propeller as a D-box-binding site. The D box of securin, but not its KEN box, is critical for securin ubiquitination by APC/C(Cdc20). Although both motifs contribute to securin ubiquitination by APC/C(Cdh1), securin mutants lacking either motif are efficiently ubiquitinated. Furthermore, D-box peptides diminish the ubiquitination of KEN-box substrates by APC/C(Cdh1), suggesting possible competition between the two motifs. Our results indicate the lack of strong positive cooperativity between the two degrons of securin. We propose that low-cooperativity, multisite target recognition enables APC/C to robustly ubiquitinate diverse substrates and helps to drive cell cycle oscillations.

    Related Citations: 
    • Cdc20: a WD40 activator for a cell cycle degradation machine
      Yu, H.
      (2007) Mol Cell 27: 3
    • KEN-box-dependent degradation of Bub1 spindle checkpoint kinase by the anaphase-promoting complex/cyclosome
      Qi, W., Yu, H.
      (2007) J Biol Chem 282: 3672
    • Mad2-independent inhibition of APC-Cdc20 by the mitotic checkpoint protein BubR1
      Tang, Z., Bharadwaj, R., Li, B., Yu, H.
      (2001) Dev Cell 1: 227
    Organizational Affiliation: 

    Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cell division cycle protein 20 homologA, B431Homo sapiensMutation(s): 0 
Gene Names: CDC20
UniProt & NIH Common Fund Data Resources
Find proteins for Q12834 (Homo sapiens)
Explore Q12834 
Go to UniProtKB:  Q12834
PHAROS:  Q12834
GTEx:  ENSG00000117399 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12834
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Mitotic checkpoint serine/threonine-protein kinase BUB1 betaC, D23Homo sapiensMutation(s): 0 
Gene Names: BUB1B, BUBR1, MAD3L, SSK1
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for O60566 (Homo sapiens)
Explore O60566 
Go to UniProtKB:  O60566
PHAROS:  O60566
GTEx:  ENSG00000156970 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60566
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.157 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.826α = 90
b = 88.129β = 99.66
c = 118.351γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-11-07
    Type: Initial release
  • Version 1.1: 2012-12-26
    Changes: Database references
  • Version 1.2: 2016-10-26
    Changes: Structure summary
  • Version 1.3: 2017-11-15
    Changes: Refinement description
  • Version 1.4: 2018-02-21
    Changes: Experimental preparation