6IGI

Crystal structure of FT condition 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.33 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.161 

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This is version 1.1 of the entry. See complete history


Literature

High-Resolution Crystal Structure of Arabidopsis FLOWERING LOCUS T Illuminates Its Phospholipid-Binding Site in Flowering.

Nakamura, Y.Lin, Y.C.Watanabe, S.Liu, Y.C.Katsuyama, K.Kanehara, K.Inaba, K.

(2019) iScience 21: 577-586

  • DOI: https://doi.org/10.1016/j.isci.2019.10.045
  • Primary Citation of Related Structures:  
    6IGG, 6IGH, 6IGI, 6IGJ

  • PubMed Abstract: 

    Arabidopsis FLOWERING LOCUS T (FT) is a pivotal component of florigen, a long-range mobile flowering signal. Here, we determined the 1.0 Å-resolution crystal structure of FT, a significantly higher-resolution crystal structure of FT than previously reported one (2.6 Å). The present crystallographic studies revealed 4 alternative configurations with the precise location of the surrounding water molecules. Using this structural data, computational docking simulation predicted the putative binding sites for phosphatidylcholine (PC), an endogenous ligand that interacts with FT to modulate flowering time. In vitro reconstitution of the lipid-protein interaction showed that mutations at two of the predicted sites significantly compromised the lipid binding ability of FT. In planta, one of the mutant FT proteins significantly affected FT function in flowering, emphasizing the involvement of PC binding in modulating FT function. Our structural, biochemical, and transgenic analyses reveal the molecular mechanism of PC binding in FT-mediated flowering time control.


  • Organizational Affiliation

    Institute of Plant and Microbial Biology, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan; Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan; Biotechnology Center, National Chung Hsing University, Taichung 402, Taiwan. Electronic address: nakamura@gate.sinica.edu.tw.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein FLOWERING LOCUS T171Arabidopsis thalianaMutation(s): 2 
Gene Names: FT
UniProt
Find proteins for Q9SXZ2 (Arabidopsis thaliana)
Explore Q9SXZ2 
Go to UniProtKB:  Q9SXZ2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9SXZ2
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EDO (Subject of Investigation/LOI)
Query on EDO

Download Ideal Coordinates CCD File 
B [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.33 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.161 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.482α = 90
b = 51.537β = 90
c = 56.908γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-25
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description