Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 100.51 kDa 
• Atom Count: 5134 
• Residue Count: 639 
• Unique protein chains: 2

4GGD

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

• DOI: 10.2210/pdb4GGD/pdb

• Classification: CELL CYCLE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2012-08-06 Released: 2012-11-07 
• Deposition Author(s): Luo, X., Tian, W., Tomchick, D.R.

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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 

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

• PubMed: 23091007 
• DOI: 10.1073/pnas.1213438109
• Structures With Same Primary Citation


• 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. 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.

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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

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Cell division cycle protein 20 homolog	A, B	431	Homo sapiens	Mutation(s): 0  Gene Names: CDC20
Find proteins for Q12834 (Homo sapiens) Go to UniProtKB:  Q12834
NIH Common Fund Data Resources
PHAROS  Q12834 GTEx  ENSG00000117399

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Mitotic checkpoint serine/threonine-protein kinase BUB1 beta	C, D	23	Homo sapiens	Mutation(s): 0  Gene Names: BUB1B, BUBR1, MAD3L, SSK1 EC: 2.7.11.1
Find proteins for O60566 (Homo sapiens) Go to UniProtKB:  O60566
NIH Common Fund Data Resources
PHAROS  O60566 GTEx  ENSG00000156970

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 = 49.826	α = 90
b = 88.129	β = 99.66
c = 118.351	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-08-06 
• Released Date: 2012-11-07 
Deposition Author(s): Luo, X., Tian, W., Tomchick, D.R.

Revision History 

• 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