Crystal Structure of Rice GID1 complexed with GA3

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

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This is version 1.4 of the entry. See complete history


Structural basis for gibberellin recognition by its receptor GID1.

Shimada, A.Ueguchi-Tanaka, M.Nakatsu, T.Nakajima, M.Naoe, Y.Ohmiya, H.Kato, H.Matsuoka, M.

(2008) Nature 456: 520-523

  • DOI: https://doi.org/10.1038/nature07546
  • Primary Citation of Related Structures:  
    3EBL, 3ED1

  • PubMed Abstract: 

    Gibberellins (GAs) are phytohormones essential for many developmental processes in plants. A nuclear GA receptor, GIBBERELLIN INSENSITIVE DWARF1 (GID1), has a primary structure similar to that of the hormone-sensitive lipases (HSLs). Here we analyse the crystal structure of Oryza sativa GID1 (OsGID1) bound with GA(4) and GA(3) at 1.9 A resolution. The overall structure of both complexes shows an alpha/beta-hydrolase fold similar to that of HSLs except for an amino-terminal lid. The GA-binding pocket corresponds to the substrate-binding site of HSLs. On the basis of the OsGID1 structure, we mutagenized important residues for GA binding and examined their binding activities. Almost all of them showed very little or no activity, confirming that the residues revealed by structural analysis are important for GA binding. The replacement of Ile 133 with Leu or Val-residues corresponding to those of the lycophyte Selaginella moellendorffii GID1s-caused an increase in the binding affinity for GA(34), a 2beta-hydroxylated GA(4). These observations indicate that GID1 originated from HSL and was further modified to have higher affinity and more strict selectivity for bioactive GAs by adapting the amino acids involved in GA binding in the course of plant evolution.

  • Organizational Affiliation

    Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Gibberellin receptor GID1
A, B, C, D, E
A, B, C, D, E, F
365Oryza sativa Japonica GroupMutation(s): 0 
Gene Names: GID1Os05g0407500LOC_Os05g33730OJ1657_H11.10P0040B10.6
EC: 3
Find proteins for Q6L545 (Oryza sativa subsp. japonica)
Explore Q6L545 
Go to UniProtKB:  Q6L545
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6L545
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on GA3

Download Ideal Coordinates CCD File 
BA [auth E]
CA [auth F]
I [auth A]
Q [auth B]
U [auth C]
BA [auth E],
CA [auth F],
I [auth A],
Q [auth B],
U [auth C],
V [auth D]
C19 H22 O6
Query on MPD

Download Ideal Coordinates CCD File 
AA [auth E]
DA [auth F]
G [auth A]
M [auth B]
R [auth C]
AA [auth E],
DA [auth F],
G [auth A],
M [auth B],
R [auth C],
W [auth D]
C6 H14 O2
Query on PO4

Download Ideal Coordinates CCD File 
P [auth B],
Z [auth E]
O4 P
Query on NO3

Download Ideal Coordinates CCD File 
EA [auth F]
FA [auth F]
H [auth A]
J [auth A]
K [auth A]
EA [auth F],
FA [auth F],
H [auth A],
J [auth A],
K [auth A],
L [auth B],
N [auth B],
O [auth B],
S [auth C],
T [auth C],
X [auth D],
Y [auth D]
N O3
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.717α = 90
b = 134.142β = 105.2
c = 118.872γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-11-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.2: 2014-03-26
    Changes: Database references
  • Version 1.3: 2017-10-25
    Changes: Refinement description
  • Version 1.4: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary