Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 58.8 kDa 
• Atom Count: 4,322 
• Modelled Residue Count: 533 
• Deposited Residue Count: 534 
• Unique protein chains: 1

 5DJ5

Crystal structure of rice DWARF14 in complex with synthetic strigolactone GR24

• PDB DOI:  https://doi.org/10.2210/pdb5DJ5/pdb

• Classification: HYDROLASE
• Organism(s): Oryza sativa Japonica Group
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-09-01 Released: 2015-10-28 
• Deposition Author(s): Zhou, X.E., Zhao, L.-H., Yi, W., Wu, Z.-S., Liu, Y., Kang, Y., Hou, L., de Waal, P.W., Li, S., Jiang, Y., Melcher, K., Xu, H.E.
• Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Natural Science Foundation of China (NSFC), Ministry of Science and Technology (MoST, China)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.224 
• R-Value Work: 0.190 
• R-Value Observed: 0.192 

Literature

Destabilization of strigolactone receptor DWARF14 by binding of ligand and E3-ligase signaling effector DWARF3.

Zhao, L.H., Zhou, X.E., Yi, W., Wu, Z., Liu, Y., Kang, Y., Hou, L., de Waal, P.W., Li, S., Jiang, Y., Scaffidi, A., Flematti, G.R., Smith, S.M., Lam, V.Q., Griffin, P.R., Wang, Y., Li, J., Melcher, K., Xu, H.E.

(2015) Cell Res 25: 1219-1236

• PubMed: 26470846 
• DOI: https://doi.org/10.1038/cr.2015.122
• Primary Citation of Related Structures:  
  5DJ5


• PubMed Abstract: 
  

Strigolactones (SLs) are endogenous hormones and exuded signaling molecules in plant responses to low levels of mineral nutrients. Key mediators of the SL signaling pathway in rice include the α/β-fold hydrolase DWARF 14 (D14) and the F-box component DWARF 3 (D3) of the ubiquitin ligase SCF(D3) that mediate ligand-dependent degradation of downstream signaling repressors. One perplexing feature is that D14 not only functions as the SL receptor but is also an active enzyme that slowly hydrolyzes diverse natural and synthetic SLs including GR24, preventing the crystallization of a binary complex of D14 with an intact SL as well as the ternary D14/SL/D3 complex. Here we overcome these barriers to derive a structural model of D14 bound to intact GR24 and identify the interface that is required for GR24-mediated D14-D3 interaction. The mode of GR24-mediated signaling, including ligand recognition, hydrolysis by D14, and ligand-mediated D14-D3 interaction, is conserved in structurally diverse SLs. More importantly, D14 is destabilized upon the binding of ligands and D3, thus revealing an unusual mechanism of SL recognition and signaling, in which the hormone, the receptor, and the downstream effectors are systematically destabilized during the signal transduction process.

---

Organizational Affiliation: 

Laboratory of Structural Sciences and Laboratory of Structural Biology and Biochemistry, Van Andel Research Institute, Grand Rapids, Michigan, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable strigolactone esterase D14	A, B	267	Oryza sativa Japonica Group	Mutation(s): 0  Gene Names: D14, D88, HTD2, Os03g0203200, LOC_Os03g10620 EC: 3.1
UniProt
Find proteins for Q10QA5 (Oryza sativa subsp. japonica) Explore Q10QA5  Go to UniProtKB:  Q10QA5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GR2	C [auth A]	(3E,3aR,8bS)-3-({[(2R)-4-methyl-5-oxo-2,5-dihydrofuran-2-yl]oxy}methylidene)-3,3a,4,8b-tetrahydro-2H-indeno[1,2-b]furan-2-one C17 H14 O5 XHSDUVBUZOUAOQ-WJQMYRPNSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
GR2	Binding MOAD:  5DJ5	IC50: 2500 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.224 
• R-Value Work: 0.190 
• R-Value Observed: 0.192 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.4	α = 90
b = 87.88	β = 90
c = 118.57	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-10-28 
Deposition Author(s): Zhou, X.E., Zhao, L.-H., Yi, W., Wu, Z.-S., Liu, Y., Kang, Y., Hou, L., de Waal, P.W., Li, S., Jiang, Y., Melcher, K., Xu, H.E.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	DK071662
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM102545
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM104212
National Natural Science Foundation of China (NSFC)	China	NSFC 31300245
National Natural Science Foundation of China (NSFC)	China	NSFC 91217311
Ministry of Science and Technology (MoST, China)	China	2012ZX09301001
Ministry of Science and Technology (MoST, China)	China	2012CB910403
Ministry of Science and Technology (MoST, China)	China	2013CB910600
Ministry of Science and Technology (MoST, China)	China	XDB08020303
Ministry of Science and Technology (MoST, China)	China	2013ZX09507001

Revision History  

• Version 1.0: 2015-10-28
  Type: Initial release
  
• Version 1.1: 2015-11-18
  Changes: Database references
• Version 1.2: 2017-09-20
  Changes: Author supporting evidence, Derived calculations
• Version 1.3: 2019-12-25
  Changes: Author supporting evidence