Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 80.32 kDa 
• Atom Count: 5826 
• Modelled Residue Count: 662 
• Deposited Residue Count: 708 
• Unique protein chains: 1

3NMW

Crystal structure of armadillo repeats domain of APC

• DOI: 10.2210/pdb3NMW/pdb

• Classification: CELL ADHESION/CELL CYCLE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-06-22 Released: 2011-07-06 
• Deposition Author(s): Zhang, Z., Chen, L., Gao, L., Lin, K., Wu, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.201 
• R-Value Work: 0.168 
• R-Value Observed: 0.170 

Literature

Structural basis for the recognition of Asef by adenomatous polyposis coli.

Zhang, Z., Chen, L., Gao, L., Lin, K., Zhu, L., Lu, Y., Shi, X., Gao, Y., Zhou, J., Xu, P., Zhang, J., Wu, G.

(2012) Cell Res 22: 372-386

• PubMed: 21788986 
• DOI: 10.1038/cr.2011.119
• Primary Citation of Related Structures:  
  3NMZ, 3NMW, 3NMX


• PubMed Abstract: 
  

Adenomatous polyposis coli (APC) regulates cell-cell adhesion and cell migration through activating the APC-stimulated guanine nucleotide-exchange factor (GEF; Asef), which is usually autoinhibited through the binding between its Src homology 3 (SH3) and Dbl homology (DH) domains. The APC-activated Asef stimulates the small GTPase Cdc42, which leads to decreased cell-cell adherence and enhanced cell migration. In colorectal cancers, truncated APC constitutively activates Asef and promotes cancer cell migration and angiogenesis. Here, we report crystal structures of the human APC/Asef complex. We find that the armadillo repeat domain of APC uses a highly conserved surface groove to recognize the APC-binding region (ABR) of Asef, conformation of which changes dramatically upon binding to APC. Key residues on APC and Asef for the complex formation were mutated and their importance was demonstrated by binding and activity assays. Structural superimposition of the APC/Asef complex with autoinhibited Asef suggests that the binding between APC and Asef might create a steric clash between Asef-DH domain and APC, which possibly leads to a conformational change in Asef that stimulates its GEF activity. Our structures thus elucidate the molecular mechanism of Asef recognition by APC, as well as provide a potential target for pharmaceutical intervention against cancers.

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Organizational Affiliation: 

State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
APC variant protein	A, B	354	Homo sapiens	Mutation(s): 0  Gene Names: APC variant protein, APC, DP2.5
UniProt & NIH Common Fund Data Resources
Find proteins for P25054 (Homo sapiens) Explore P25054  Go to UniProtKB:  P25054
PHAROS:  P25054 GTEx:  ENSG00000134982

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.201 
• R-Value Work: 0.168 
• R-Value Observed: 0.170 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.389	α = 90.31
b = 52.682	β = 89.95
c = 63.451	γ = 95.16

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-06-22 
• Released Date: 2011-07-06 
Deposition Author(s): Zhang, Z., Chen, L., Gao, L., Lin, K., Wu, G.

Revision History  

• Version 1.0: 2011-07-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2016-12-21
  Changes: Structure summary
• Version 1.3: 2017-03-15
  Changes: Database references
• Version 1.4: 2019-12-25
  Changes: Advisory, Database references, Derived calculations