Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 38.68 kDa 
• Atom Count: 2444 
• Modelled Residue Count: 301 
• Deposited Residue Count: 344 
• Unique protein chains: 1

3AU3

Crystal structure of armadillo repeat domain of APC

• PDB DOI: 10.2210/pdb3AU3/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2011-01-28 Released: 2011-11-02 
• Deposition Author(s): Murayama, K., Kato-Murayama, M., Terada, T., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.232 
• R-Value Work: 0.204 
• R-Value Observed: 0.204 

Literature

Crystal structures of the armadillo repeat domain of adenomatous polyposis coli and its complex with the tyrosine-rich domain of sam68

Morishita, E.C., Murayama, K., Kato-Murayama, M., Ishizuka-Katsura, Y., Tomabechi, Y., Hayashi, T., Terada, T., Handa, N., Shirouzu, M., Akiyama, T., Yokoyama, S.

(2011) Structure 19: 1496-1508

• PubMed: 22000517 
• DOI: 10.1016/j.str.2011.07.013
• Primary Citation of Related Structures:  
  3AU3, 3QHE


• PubMed Abstract: 
  

Adenomatous polyposis coli (APC) is a tumor suppressor protein commonly mutated in colorectal tumors. APC plays important roles in Wnt signaling and other cellular processes. Here, we present the crystal structure of the armadillo repeat (Arm) domain of APC, which facilitates the binding of APC to various proteins. APC-Arm forms a superhelix with a positively charged groove. We also determined the structure of the complex of APC-Arm with the tyrosine-rich (YY) domain of the Src-associated in mitosis, 68 kDa protein (Sam68), which regulates TCF-1 alternative splicing. Sam68-YY forms numerous interactions with the residues on the groove and is thereby fixed in a bent conformation. We assessed the effects of mutations and phosphorylation on complex formation between APC-Arm and Sam68-YY. Structural comparisons revealed different modes of ligand recognition between the Arm domains of APC and other Arm-containing proteins.

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Organizational Affiliation: 

RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenomatous polyposis coli protein	A	344	Homo sapiens	Mutation(s): 0  Gene Names: APC, DP2.5
UniProt & NIH Common Fund Data Resources
Find proteins for P25054 (Homo sapiens) Explore P25054  Go to UniProtKB:  P25054
PHAROS:  P25054

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.232 
• R-Value Work: 0.204 
• R-Value Observed: 0.204 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.327	α = 90
b = 114.327	β = 90
c = 61.821	γ = 120

Software Package:

Software Name	Purpose
SOLVE	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-01-28 
• Released Date: 2011-11-02 
Deposition Author(s): Murayama, K., Kato-Murayama, M., Terada, T., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2011-11-02
  Type: Initial release