8VGB

Crystal Structure of Guanine Nucleotide-Binding Protein Alpha Subunit (G Protein) from Oryza sativa in complex with GDP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.266 
  • R-Value Observed: 0.269 

Starting Model: in silico
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Ligand Structure Quality Assessment 


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Literature

Structure-function analysis of plant G-protein regulatory mechanisms identifies key G alpha-RGS protein interactions.

Torres-Rodriguez, M.D.Lee, S.G.Roy Choudhury, S.Paul, R.Selvam, B.Shukla, D.Jez, J.M.Pandey, S.

(2024) J Biol Chem 300: 107252-107252

  • DOI: https://doi.org/10.1016/j.jbc.2024.107252
  • Primary Citation of Related Structures:  
    8VGA, 8VGB

  • PubMed Abstract: 

    Heterotrimeric GTP-binding protein alpha subunit (Gα) and its cognate regulator of G-protein signaling (RGS) protein transduce signals in eukaryotes spanning protists, amoeba, animals, fungi, and plants. The core catalytic mechanisms of the GTPase activity of Gα and the interaction interface with RGS for the acceleration of GTP hydrolysis seem to be conserved across these groups; however, the RGS gene is under low selective pressure in plants, resulting in its frequent loss. Our current understanding of the structural basis of Gα:RGS regulation in plants has been shaped by Arabidopsis Gα, (AtGPA1), which has a cognate RGS protein. To gain a comprehensive understanding of this regulation beyond Arabidopsis, we obtained the x-ray crystal structures of Oryza sativa Gα, which has no RGS, and Selaginella moellendorffi (a lycophyte) Gα that has low sequence similarity with AtGPA1 but has an RGS. We show that the three-dimensional structure, protein-protein interaction with RGS, and the dynamic features of these Gα are similar to AtGPA1 and metazoan Gα. Molecular dynamic simulation of the Gα-RGS interaction identifies the contacts established by specific residues of the switch regions of GTP-bound Gα, crucial for this interaction, but finds no significant difference due to specific amino acid substitutions. Together, our data provide valuable insights into the regulatory mechanisms of plant G-proteins but do not support the hypothesis of adaptive co-evolution of Gα:RGS proteins in plants.


  • Organizational Affiliation

    Donald Danforth Plant Science Center, St Louis, Missouri, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein alpha-1 subunit
A, B, C, D
383Oryza sativa Indica GroupMutation(s): 0 
Gene Names: GPA1D1GA1RGA1OsI_018808
UniProt
Find proteins for A2Y3B5 (Oryza sativa subsp. indica)
Explore A2Y3B5 
Go to UniProtKB:  A2Y3B5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA2Y3B5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GDP (Subject of Investigation/LOI)
Query on GDP

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
I [auth C],
K [auth D]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B],
J [auth C],
L [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.266 
  • R-Value Observed: 0.269 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.393α = 90
b = 68.419β = 89.91
c = 167.977γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data collection
PHASERphasing
Cootmodel building
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-06
    Type: Initial release