4AIW

GAPR-1 with bound inositol hexakisphosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.152 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Interaction of Gapr-1 with Lipid Bilayers is Regulated by Alternative Homodimerization.

Van Galen, J.Olrichs, N.K.Schouten, A.Serrano, R.L.Nolte-'T Hoen, E.N.M.Eerland, R.Kaloyanova, D.Gros, P.Helms, J.B.

(2012) Biochim.Biophys.Acta 1818: 2175

  • DOI: 10.1016/j.bbamem.2012.04.016

  • PubMed Abstract: 
  • Golgi-Associated Plant Pathogenesis-Related protein 1 (GAPR-1) is a mammalian protein that belongs to the superfamily of plant pathogenesis related proteins group 1 (PR-1). GAPR-1 is a peripheral membrane-binding protein that strongly associates with ...

    Golgi-Associated Plant Pathogenesis-Related protein 1 (GAPR-1) is a mammalian protein that belongs to the superfamily of plant pathogenesis related proteins group 1 (PR-1). GAPR-1 is a peripheral membrane-binding protein that strongly associates with lipid-enriched microdomains at the cytosolic leaflet of Golgi membranes. Little is known about the mechanism of GAPR-1 interaction with membranes. We previously suggested that dimerization plays a role in the function of GAPR-1 and here we report that phytic acid (inositol hexakisphosphate) induces dimerization of GAPR-1 in solution. Elucidation of the crystal structure of GAPR-1 in the presence of phytic acid revealed that the GAPR-1 dimer differs from the previously published GAPR-1 dimer structure. In this structure, one of the monomeric subunits of the crystallographic dimer is rotated by 28.5°. To study the GAPR-1 dimerization properties, we investigated the interaction with liposomes in a light scattering assay and by flow cytometry. In the presence of negatively charged lipids, GAPR-1 caused a rapid and stable tethering of liposomes. [D81K]GAPR-1, a mutant predicted to stabilize the IP6-induced dimer conformation, also caused tethering of liposomes. [A68K]GAPR-1 however, a mutant predicted to stabilize the non-rotated dimer conformation, is capable of binding to liposomes but did not cause liposome tethering. Our combined data suggest that the charge properties of the lipid bilayer can regulate GAPR-1 dynamics as a potential mechanism to modulate GAPR-1 function.


    Related Citations: 
    • Structural Analysis of the Human Golgi-Associated Plant Pathogenesis Related Protein Gapr-1 Implicates Dimerization as a Regulatory Mechanism.
      Serrano, R.L.,Kuhn, A.,Hendricks, A.,Helms, J.B.,Sinning, I.,Groves, M.R.
      (2004) J.Mol.Biol. 339: 173


    Organizational Affiliation

    Department of Biochemistry and Cell Biology, Utrecht University, Utrecht, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GOLGI-ASSOCIATED PLANT PATHOGENESIS-RELATED PROTEIN 1
A
154Homo sapiensMutation(s): 0 
Gene Names: GLIPR2 (C9orf19, GAPR1)
Find proteins for Q9H4G4 (Homo sapiens)
Go to Gene View: GLIPR2
Go to UniProtKB:  Q9H4G4
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
I6P
Query on I6P

Download SDF File 
Download CCD File 
A
INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE
MYO-INOSITOL HEXAKISPHOSPHATE
C6 H18 O24 P6
IMQLKJBTEOYOSI-GPIVLXJGSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
OCS
Query on OCS
A
L-PEPTIDE LINKINGC3 H7 N O5 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.152 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 44.088α = 90.00
b = 64.872β = 90.00
c = 103.059γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
MOSFLMdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-08-08
    Type: Initial release
  • Version 1.1: 2019-01-30
    Type: Data collection, Experimental preparation, Other
  • Version 1.2: 2019-02-06
    Type: Data collection, Experimental preparation