Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 19.46 kDa 
• Atom Count: 1489 
• Modelled Residue Count: 167 
• Deposited Residue Count: 171 
• Unique protein chains: 1

6IGJ

Crystal structure of FT condition 4

• PDB DOI: 10.2210/pdb6IGJ/pdb

• Classification: PLANT PROTEIN
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2018-09-25 Released: 2019-12-25 
• Deposition Author(s): Watanabe, S., Nakamura, Y., Kanehara, K., Inaba, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.225 
• R-Value Work: 0.197 
• R-Value Observed: 0.198 

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

• PubMed: 31726375 
• DOI: 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.

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Organizational Affiliation: 

Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan; CREST, Japan Science and Technology Agency, Kawaguchi 332-0012, Japan. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein FLOWERING LOCUS T	A	171	Arabidopsis thaliana	Mutation(s): 2  Gene Names: FT, At1g65480, F5I14.3
UniProt
Find proteins for Q9SXZ2 (Arabidopsis thaliana) Explore Q9SXZ2  Go to UniProtKB:  Q9SXZ2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.225 
• R-Value Work: 0.197 
• R-Value Observed: 0.198 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.503	α = 90
b = 53.503	β = 90
c = 103.975	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2018-09-25 
• Released Date: 2019-12-25 
Deposition Author(s): Watanabe, S., Nakamura, Y., Kanehara, K., Inaba, K.

Revision History  

• Version 1.0: 2019-12-25
  Type: Initial release