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 
  • R-Value Observed: 0.187 

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:  
    3NG8, 3N4W, 2QT7

  • 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 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 ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Receptor-type tyrosine-protein phosphatase-like N AB89Homo sapiensMutation(s): 1 
Gene Names: ICA3ICA512PTPRN
Find proteins for Q16849 (Homo sapiens)
Explore Q16849 
Go to UniProtKB:  Q16849
NIH Common Fund Data Resources
PHAROS:  Q16849
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download Ideal Coordinates 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 
  • R-Value Observed: 0.187 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 31.472α = 90
b = 66.016β = 90
c = 73.65γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

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