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 
  • R-Value Observed: 0.182 

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:  
    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 ...

    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 the Department of Chemistry, University of Hamburg, 22607 Hamburg, Germany petri.kursula@oulu.fi.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN AHNAK2A, B97Homo sapiensMutation(s): 0 
Gene Names: AHNAK2C14orf78KIAA2019
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IVF2 (Homo sapiens)
Explore Q8IVF2 
Go to UniProtKB:  Q8IVF2
PHAROS:  Q8IVF2
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PG4
Query on PG4

Download Ideal Coordinates CCD File 
C [auth A], D [auth A], E [auth A]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

Download Ideal Coordinates CCD File 
F [auth B]POTASSIUM ION
K
NPYPAHLBTDXSSS-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 
  • 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
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

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

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