3ED1 | pdb_00003ed1

Crystal Structure of Rice GID1 complexed with GA3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.239 (Depositor), 0.242 (DCC) 
  • R-Value Work: 
    0.197 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 
    0.199 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 3ED1

Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

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 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.

Macromolecule Content 

  • Total Structure Weight: 249.13 kDa 
  • Atom Count: 15,936 
  • Modeled Residue Count: 1,871 
  • Deposited Residue Count: 2,190 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
UniProt
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
Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GA3

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]
GIBBERELLIN A3
C19 H22 O6
IXORZMNAPKEEDV-OBDJNFEBSA-N
MPD

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]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
PO4

Query on PO4



Download:Ideal Coordinates CCD File
P [auth B],
Z [auth E]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
NO3

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]
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.239 (Depositor), 0.242 (DCC) 
  • R-Value Work:  0.197 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 0.199 (Depositor) 
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
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing

Structure Validation

View Full Validation Report



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