4RJ9

Structure of a plant specific C2 domain protein, OsGAP1 from rice


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Site-directed Mutagenesis Shows the Significance of Interactions with Phospholipids and the G-protein OsYchF1 for the Physiological Functions of the Rice GTPase-activating Protein 1 (OsGAP1).

Yung, Y.L.Cheung, M.Y.Miao, R.Fong, Y.H.Li, K.P.Yu, M.H.Chye, M.L.Wong, K.B.Lam, H.M.

(2015) J Biol Chem 290: 23984-23996

  • DOI: https://doi.org/10.1074/jbc.M115.655639
  • Primary Citation of Related Structures:  
    4RJ9

  • PubMed Abstract: 

    The C2 domain is one of the most diverse phospholipid-binding domains mediating cellular signaling. One group of C2-domain proteins are plant-specific and are characterized by their small sizes and simple structures. We have previously reported that a member of this group, OsGAP1, is able to alleviate salt stress and stimulate defense responses, and bind to both phospholipids and an unconventional G-protein, OsYchF1. Here we solved the crystal structure of OsGAP1 to a resolution of 1.63 Å. Using site-directed mutagenesis, we successfully differentiated between the clusters of surface residues that are required for binding to phospholipids versus OsYchF1, which, in turn, is critical for its role in stimulating defense responses. On the other hand, the ability to alleviate salt stress by OsGAP1 is dependent only on its ability to bind OsYchF1 and is independent of its phospholipid-binding activity.


  • Organizational Affiliation

    From the School of Life Sciences, Centre for Soybean Research of the Partner State Key Laboratory of Agrobiotechnology, and.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
C2 domain-containing protein-like165Oryza sativa Japonica GroupMutation(s): 0 
Gene Names: Os02g0327000OsGAP1OSJNBb0042G06.10OsJ_06508P0476C12.36
EC: 6.5.1.1
Membrane Entity: Yes 
UniProt
Find proteins for Q6YWF1 (Oryza sativa subsp. japonica)
Explore Q6YWF1 
Go to UniProtKB:  Q6YWF1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6YWF1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.19α = 90
b = 166.75β = 90
c = 60.73γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
PHASESphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-08-26
    Type: Initial release
  • Version 1.1: 2015-09-02
    Changes: Database references
  • Version 1.2: 2015-10-21
    Changes: Database references
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description