Crystal structure of afadin PDZ domain in complex with the C-terminal peptide from nectin-3

Experimental Data Snapshot

  • Resolution: 2.78 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.241 

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This is version 1.3 of the entry. See complete history


Crystal structure of afadin PDZ domain-nectin-3 complex shows the structural plasticity of the ligand-binding site.

Fujiwara, Y.Goda, N.Tamashiro, T.Narita, H.Satomura, K.Tenno, T.Nakagawa, A.Oda, M.Suzuki, M.Sakisaka, T.Takai, Y.Hiroaki, H.

(2015) Protein Sci 24: 376-385

  • DOI: https://doi.org/10.1002/pro.2628
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Afadin, a scaffold protein localized in adherens junctions (AJs), links nectins to the actin cytoskeleton. Nectins are the major cell adhesion molecules of AJs. At the initial stage of cell-cell junction formation, the nectin-afadin interaction plays an indispensable role in AJ biogenesis via recruiting and tethering other components. The afadin PDZ domain (AFPDZ) is responsible for binding the cytoplasmic C-terminus of nectins. AFPDZ is a class II PDZ domain member, which prefers ligands containing a class II PDZ-binding motif, X-Φ-X-Φ (Φ, hydrophobic residues); both nectins and other physiological AFPDZ targets contain this class II motif. Here, we report the first crystal structure of the AFPDZ in complex with the nectin-3 C-terminal peptide containing the class II motif. We engineered the nectin-3 C-terminal peptide and AFPDZ to produce an AFPDZ-nectin-3 fusion protein and succeeded in obtaining crystals of this complex as a dimer. This novel dimer interface was created by forming an antiparallel β sheet between β2 strands. A major structural change compared with the known AFPDZ structures was observed in the α2 helix. We found an approximately 2.5 Å-wider ligand-binding groove, which allows the PDZ to accept bulky class II ligands. Apparently, the last three amino acids of the nectin-3 C-terminus were sufficient to bind AFPDZ, in which the two hydrophobic residues are important.

  • Organizational Affiliation

    Division of Structural Biology, Graduate School of Medicine, Kobe University, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, Hyogo, 650-0017, Japan; Research Center for Structural and Functional Proteomics, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, 565-0871, Japan; Global-COE (Center of Excellence) Program for Integrative Membrane Biology, Kobe University, 7-5-1 Kusunoki-cho, Chuo, Kobe, Hyogo, 650-0017, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Afadin, Nectin-3
A, B
106Mus musculusMutation(s): 0 
Gene Names: Mllt4Af6
UniProt & NIH Common Fund Data Resources
Find proteins for Q9QZQ1 (Mus musculus)
Explore Q9QZQ1 
Go to UniProtKB:  Q9QZQ1
IMPC:  MGI:1314653
Find proteins for Q9JLB9 (Mus musculus)
Explore Q9JLB9 
Go to UniProtKB:  Q9JLB9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ9QZQ1Q9JLB9
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.78 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.241 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.477α = 90
b = 90.481β = 90
c = 88.745γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-04-25
    Type: Initial release
  • Version 1.1: 2015-03-11
    Changes: Database references
  • Version 1.2: 2017-08-23
    Changes: Refinement description, Source and taxonomy
  • Version 1.3: 2023-11-01
    Changes: Data collection, Database references, Refinement description