7WA4

Crystal structure of GIGANTEA in complex with LKP2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.250 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structural analysis of the regulation of blue-light receptors by GIGANTEA.

Kwon, E.Pathak, D.Dahal, P.Tandukar, S.Jung, H.S.Kim, W.Y.Kim, D.Y.

(2022) Cell Rep 39: 110700-110700

  • DOI: https://doi.org/10.1016/j.celrep.2022.110700
  • Primary Citation of Related Structures:  
    7WA4

  • PubMed Abstract: 

    In Arabidopsis, GIGANTEA (GI), together with the blue-light receptors ZTL, LKP2, and FKF1, regulates degradation of the core clock protein TOC1 and the flowering repressor CDFs, thereby controlling circadian oscillation and flowering. Despite the significance of GI in diverse plant physiology, its molecular function is not much understood because of technical problems in protein preparation and a lack of structural information. Here, we report the purification of the GI monomer and the crystal structure of the GI/LKP2 complex. The crystal structure reveals that residues 1-813 of GI possess an elongated rigid structure formed by stacking hydrophobic α-helices and that the LOV domain of LKP2 binds to the middle region of the GI (residues 563-789). Interaction analysis further shows that LOV homodimers are converted to monomers by GI binding. Our results provide structural insights into the regulation of the circadian clock and photoperiodic flowering by GI and ZTL/LKP2/FKF1.


  • Organizational Affiliation

    College of Pharmacy, Yeungnam University, Gyeongsan 38541, Republic of Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein GIGANTEA815Arabidopsis thalianaMutation(s): 0 
Gene Names: GIAt1g22770T22J18.6
UniProt
Find proteins for Q9SQI2 (Arabidopsis thaliana)
Explore Q9SQI2 
Go to UniProtKB:  Q9SQI2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9SQI2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Adagio protein 2138Arabidopsis thalianaMutation(s): 0 
Gene Names: ADO2FKL1LKP2At2g18915F19F24.11
UniProt
Find proteins for Q8W420 (Arabidopsis thaliana)
Explore Q8W420 
Go to UniProtKB:  Q8W420
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8W420
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

Download Ideal Coordinates CCD File 
C [auth B]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.250 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.75α = 90
b = 104.75β = 90
c = 232.161γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
Aimlessdata scaling
AutoSolphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-27
    Type: Initial release
  • Version 1.1: 2022-05-04
    Changes: Database references