An intertwined homodimer of the PDZ homology domain of AHNAK2

Experimental Data Snapshot

  • Resolution: 1.75 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 

wwPDB Validation   3D Report Full Report

This is version 1.6 of the entry. See complete history


Periaxin and Ahnak Nucleoprotein 2 Form Intertwined Homodimers Through Domain Swapping

Han, H.Kursula, P.

(2014) J Biol Chem 289: 14121

  • DOI: https://doi.org/10.1074/jbc.M114.554816
  • Primary Citation of Related Structures:  
    4CMZ, 4CN0

  • PubMed Abstract: 

    Periaxin (PRX) is an abundant protein in the peripheral nervous system, with an important role in myelination. PRX participates in large molecular complexes, most likely through the interactions of its N-terminal PSD-95/Discs-large/ZO-1 (PDZ)-like domain. We present the crystal structures of the PDZ-like domains from PRX and its homologue AHNAK nucleoprotein 2 (AHNAK2). The unique intertwined, domain-swapped dimers provide a structural basis for the homodimerization of both proteins. The core of the homodimer is formed by a 6-stranded antiparallel β sheet, with every other strand from a different chain. The AHNAK2 PDZ domain structure contains a bound class III ligand peptide. The binding pocket is preformed, and the peptide-PDZ interactions have unique aspects, including two salt bridges and weak recognition of the peptide C terminus. Tight homodimerization may be central to the scaffolding functions of PRX and AHNAK2 in molecular complexes linking the extracellular matrix to the cytoskeletal network.

  • Organizational Affiliation

    From the Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, 90014 Oulu, Finland, the German Electron Synchrotron (DESY), 22607 Hamburg, Germany, and.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
97Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IVF2 (Homo sapiens)
Explore Q8IVF2 
Go to UniProtKB:  Q8IVF2
GTEx:  ENSG00000185567 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IVF2
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.75 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.73α = 90
b = 81.73β = 90
c = 65.31γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-04-02
    Type: Initial release
  • Version 1.1: 2014-04-09
    Changes: Database references
  • Version 1.2: 2014-04-23
    Changes: Atomic model
  • Version 1.3: 2014-08-27
    Changes: Database references
  • Version 1.4: 2014-12-17
    Changes: Data collection
  • Version 1.5: 2018-03-07
    Changes: Data collection, Source and taxonomy
  • Version 1.6: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description