8Z53 | pdb_00008z53

Arabidopsis Dwarf14 (AtD14) co-crystallized in the presence of Zaxinone

• PDB DOI: https://doi.org/10.2210/pdb8Z53/pdb

• Classification: HYDROLASE
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2024-04-18 Released: 2025-04-23 
• Deposition Author(s): Arold, S.T., Shahul Hameed, U.F.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.226 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: experimental

Literature

Arabidopsis response to the apocarotenoid zaxinone involves interference with strigolactone signaling via binding to DWARF14.

Moreno, J.C., Shahul Hameed, U.F., Balakrishna, A., Ablazov, A., Liew, K.X., Jamil, M., Mi, J., Alashoor, K., de Saint Germain, A., Arold, S.T., Al-Babili, S.

(2025) Nat Commun 16: 8789-8789

• PubMed: 41038837 
• DOI: https://doi.org/10.1038/s41467-025-63845-w
• Primary Citation of Related Structures:  
  8Z53


• PubMed Abstract: 
  

  The natural growth regulator zaxinone increases the levels of the phytohormones strigolactone (SL) and abscisic acid in Arabidopsis (Arabidopsis thaliana) via unknown mechanisms. Here we demonstrate that part of the effect of zaxinone in Arabidopsis depend on the SL receptor DWARF14 (AtD14) and the F-Box protein MORE AXILLARY BRANCHING2 (AtMAX2) that mediate the signaling of SLs and karrikins. Binding assays and co-crystallization reveal zaxinone as an additional ligand of AtD14 and an SL antagonist that interrupts the interaction of AtD14 with AtMAX2. Zaxinone also binds to the karrikin receptor KARRIKIN INSENSITIVE2 (AtKAI2). These findings unveil a perception mechanism for zaxinone in Arabidopsis and demonstrate the capability of AtD14 to bind signaling molecules, other than strigolactones and mediate their transduction.

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Organizational Affiliation: 
• The Bioactives Laboratory, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.
Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
Computational Biology Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.
State Key Laboratory of Traditional Chinese Medicine Syndrome, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Chinese Medicine, Guangdong Provincial Academy of Chinese Medical Sciences, Guangzhou, China.
Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France.
Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia. [e-mail].
Computational Biology Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia. [e-mail].
The Bioactives Laboratory, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia. [e-mail].
Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 59.48 kDa 
• Atom Count: 4,238 
• Modeled Residue Count: 527 
• Deposited Residue Count: 530 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Strigolactone esterase D14	A, B	265	Arabidopsis thaliana	Mutation(s): 0  Gene Names: D14, At3g03990, T11I18.10 EC: 3.1
UniProt
Find proteins for Q9SQR3 (Arabidopsis thaliana) Explore Q9SQR3  Go to UniProtKB:  Q9SQR3

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1L1M (Subject of Investigation/LOI)	C [auth A], F [auth B]	(7E)-6-methyl-8-[(4S)-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octa-3,5,7-trien-2-one C18 H26 O2 JLNMEHQAHDSEEE-FRIDJMAZSA-N
PEG	D [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL (Subject of Investigation/LOI)	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.226 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.82	α = 90
b = 69.58	β = 92.85
c = 89.86	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-04-23 
Deposition Author(s): Arold, S.T., Shahul Hameed, U.F.

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Funding Organization	Location	Grant Number
Other private	Saudi Arabia	King Abdullah University of Science and Technology

Revision History  

• Version 1.0: 2025-04-23
  Type: Initial release
  
• Version 2.0: 2025-06-11
  Type: Coordinate replacement
  Reason: Ligand geometry
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Other, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
• Version 2.1: 2025-11-12
  Changes: Database references, Structure summary