4HTI

Crystallographic structure of the membrane-proximal ectodomain of the human receptor-type protein-tyrosine phosphatase phogrin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.954 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

X-ray structure of the mature ectodomain of phogrin.

Noguera, M.E.Primo, M.E.Jakoncic, J.Poskus, E.Solimena, M.Ermacora, M.R.

(2015) J.Struct.Funct.Genom. 16: 1-9

  • DOI: 10.1007/s10969-014-9191-0
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Phogrin/IA-2β and ICA512/IA-2 are two paralogs receptor-type protein-tyrosine phosphatases (RPTP) that localize in secretory granules of various neuroendocrine cells. In pancreatic islet β-cells, they participate in the regulation of insulin secretio ...

    Phogrin/IA-2β and ICA512/IA-2 are two paralogs receptor-type protein-tyrosine phosphatases (RPTP) that localize in secretory granules of various neuroendocrine cells. In pancreatic islet β-cells, they participate in the regulation of insulin secretion, ensuring proper granulogenesis, and β-cell proliferation. The role of their cytoplasmic tail has been partially unveiled, while that of their luminal region remains unclear. To advance the understanding of its structure-function relationship, the X-ray structure of the mature ectodomain of phogrin (ME phogrin) at pH 7.4 and 4.6 has been solved at 1.95- and 2.01-Å resolution, respectively. Similarly to the ME of ICA512, ME phogrin adopts a ferredoxin-like fold: a sheet of four antiparallel β-strands packed against two α-helices. Sequence conservation among vertebrates, plants and insects suggests that the structural similarity extends to all the receptor family. Crystallized ME phogrin is monomeric, in agreement with solution studies but in striking contrast with the behavior of homodimeric ME ICA512. The structural details that may cause the quaternary structure differences are analyzed. The results provide a basis for building models of the overall orientation and oligomerization state of the receptor in biological membranes.


    Organizational Affiliation

    Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Sáenz Peña 352, B1876BXD, Bernal, Buenos Aires, Argentina.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Receptor-type tyrosine-protein phosphatase N2
A
99Homo sapiensMutation(s): 0 
Gene Names: PTPRN2 (KIAA0387)
EC: 3.1.3.-, 3.1.3.48
Find proteins for Q92932 (Homo sapiens)
Go to Gene View: PTPRN2
Go to UniProtKB:  Q92932
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.954 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.221 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 55.133α = 90.00
b = 55.133β = 90.00
c = 148.391γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
REFMACrefinement
HKL-2000data collection
MOLREPphasing
HKL-2000data reduction
HKL-2000data scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-11-28
    Type: Initial release
  • Version 1.1: 2012-12-19
    Type: Database references
  • Version 1.2: 2013-03-20
    Type: Database references
  • Version 1.3: 2013-07-24
    Type: Database references
  • Version 1.4: 2015-03-18
    Type: Database references
  • Version 1.5: 2017-11-15
    Type: Refinement description