4CN0

An intertwined homodimer of the PDZ homology domain of AHNAK2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

Periaxin and Ahnak Nucleoprotein 2 Form Intertwined Homodimers Through Domain Swapping

Han, H.Kursula, P.

(2014) J.Biol.Chem. 289: 14121

  • DOI: 10.1074/jbc.M114.554816
  • Primary Citation of Related Structures:  

  • 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 do ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN AHNAK2
A, B
97Homo sapiensMutation(s): 0 
Gene Names: AHNAK2 (C14orf78, KIAA2019)
Find proteins for Q8IVF2 (Homo sapiens)
Go to Gene View: AHNAK2
Go to UniProtKB:  Q8IVF2
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
B
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
PG4
Query on PG4

Download SDF File 
Download CCD File 
A
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.180 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 81.730α = 90.00
b = 81.730β = 90.00
c = 65.310γ = 120.00
Software Package:
Software NamePurpose
XDSdata scaling
XDSdata reduction
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2014-01-20 
  • Released Date: 2014-04-02 
  • Deposition Author(s): Han, H., Kursula, P.

Revision History 

  • Version 1.0: 2014-04-02
    Type: Initial release
  • Version 1.1: 2014-04-09
    Type: Database references
  • Version 1.2: 2014-04-23
    Type: Atomic model
  • Version 1.3: 2014-08-27
    Type: Database references
  • Version 1.4: 2014-12-17
    Type: Data collection
  • Version 1.5: 2018-03-07
    Type: Data collection, Source and taxonomy