4AIW | pdb_00004aiw

GAPR-1 with bound inositol hexakisphosphate

• PDB DOI: https://doi.org/10.2210/pdb4AIW/pdb

• Classification: LIPID BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2012-02-15 Released: 2012-08-08 
• Deposition Author(s): Schouten, A., Gros, P., Helms, J.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.187 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.152 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.154 (Depositor) 

Starting Model: experimental

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

• PubMed: 22560898 
• DOI: https://doi.org/10.1016/j.bbamem.2012.04.016
• Primary Citation of Related Structures:  
  4AIW


• 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 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 17.95 kDa 
• Atom Count: 1,434 
• Modelled Residue Count: 151 
• Deposited Residue Count: 154 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GOLGI-ASSOCIATED PLANT PATHOGENESIS-RELATED PROTEIN 1	A	154	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H4G4 (Homo sapiens) Explore Q9H4G4  Go to UniProtKB:  Q9H4G4
PHAROS:  Q9H4G4 GTEx:  ENSG00000122694

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IHP	B [auth A]	INOSITOL HEXAKISPHOSPHATE C6 H18 O24 P6 IMQLKJBTEOYOSI-GPIVLXJGSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
OCS	A	L-PEPTIDE LINKING	C3 H7 N O5 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.187 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.152 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.154 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.088	α = 90
b = 64.872	β = 90
c = 103.059	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-08 
Deposition Author(s): Schouten, A., Gros, P., Helms, J.B.

Revision History  

• Version 1.0: 2012-08-08
  Type: Initial release
  
• Version 1.1: 2019-01-30
  Changes: Data collection, Experimental preparation, Other
• Version 1.2: 2019-02-06
  Changes: Data collection, Experimental preparation
• Version 2.0: 2020-10-07
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Structure summary
• Version 2.1: 2023-12-20
  Changes: Data collection, Database references, Refinement description