Crystal structure of armadillo repeats domain of APC

Experimental Data Snapshot

  • Resolution: 1.60 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 

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This is version 1.5 of the entry. See complete history


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

  • DOI: https://doi.org/10.1038/cr.2011.119
  • Primary Citation of Related Structures:  
    3NMW, 3NMX, 3NMZ

  • 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.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
APC variant protein
A, B
354Homo sapiensMutation(s): 0 
Gene Names: APC variant protein
UniProt & NIH Common Fund Data Resources
Find proteins for P25054 (Homo sapiens)
Explore P25054 
Go to UniProtKB:  P25054
GTEx:  ENSG00000134982 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25054
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
A, B
Experimental Data & Validation

Experimental Data

  • 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 = 51.389α = 90.31
b = 52.682β = 89.95
c = 63.451γ = 95.16
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.5: 2023-12-27
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description