3N4W

Crystal structure of an abridged SER to ALA mutant of the mature ectodomain of the human receptor-type protein-tyrosine phosphatase ICA512/IA-2 at pH 7.5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of the mature ectodomain of the human receptor-type protein-tyrosine phosphatase IA-2.

Primo, M.E.Klinke, S.Sica, M.P.Goldbaum, F.A.Jakoncic, J.Poskus, E.Ermacora, M.R.

(2008) J.Biol.Chem. 283: 4674-4681

  • DOI: 10.1074/jbc.M708144200
  • Primary Citation of Related Structures:  
  • Also Cited By: 3NP5, 3NG8, 3N4W, 3N01

  • PubMed Abstract: 
  • IA-2 (insulinoma-associated protein 2) is a protein-tyrosine phosphatase receptor located in secretory granules of neuroendocrine cells. Initially, it attracted attention due to its involvement in the autoimmune response associated to diabetes. Later ...

    IA-2 (insulinoma-associated protein 2) is a protein-tyrosine phosphatase receptor located in secretory granules of neuroendocrine cells. Initially, it attracted attention due to its involvement in the autoimmune response associated to diabetes. Later it was found that upon exocytosis, the cytoplasmic domain of IA-2 is cleaved and relocated to the nucleus, where it enhances the transcription of the insulin gene. A concerted functioning of the whole receptor is to be expected. However, very little is known about the structure and function of the transmembrane and extracellular domains of IA-2. To address this issue, we solved the x-ray structure of the mature ectodomain of IA-2 (meIA-2) to 1.30A resolution. The fold of meIA-2 is related to the SEA (sea urchin sperm protein, enterokinase, agrin)) domains of mucins, suggesting its participation in adhesive contacts to the extracellular matrix and providing clues on how this kind of molecule may associate and form homo- and heterodimers. Moreover, we discovered that meIA-2 is self-proteolyzed in vitro by reactive oxygen species, suggesting the possibility of a new shedding mechanism that might be significant in normal function or pathological processes. Knowledge of meIA-2 structure should facilitate the search of its possible ligands and molecular interactions.


    Related Citations: 
    • Structure of the mature ectodomain of the human receptor-type protein-tyrosine phosphatase IA-2
      Primo, M.E.,Klinke, S.,Sica, M.P.,Goldbaum, F.A.,Jakoncic, J.,Poskus, E.,Ermacora, M.R.
      (2008) J.Biol.Chem. 283: 4674


    Organizational Affiliation

    Consejo Nacional de Investigaciones Científicas y Técnicas (Conicet), Rivadavia 1917 C1033AAJ, Ciudad Autónoma de Buenos Aires, Argentina.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Receptor-type tyrosine-protein phosphatase-like N
A, B
89Homo sapiensMutation(s): 1 
Gene Names: PTPRN (ICA3, ICA512)
Find proteins for Q16849 (Homo sapiens)
Go to Gene View: PTPRN
Go to UniProtKB:  Q16849
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 31.472α = 90.00
b = 66.016β = 90.00
c = 73.650γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
HKL-2000data scaling
DENZOdata reduction
HKL-2000data reduction
PDB_EXTRACTdata extraction
REFMACrefinement
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-12-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2013-07-10
    Type: Database references
  • Version 1.3: 2017-11-08
    Type: Advisory, Refinement description