5DJ5

Crystal structure of rice DWARF14 in complex with synthetic strigolactone GR24


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 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


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

  • 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

    VARI-SIMM Center, Center for Structure and Function of Drug Targets, Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Probable strigolactone esterase D14
A, B
267Oryza sativa Japonica GroupMutation(s): 0 
Gene Names: D14D88HTD2Os03g0203200LOC_Os03g10620
EC: 3.1
UniProt
Find proteins for Q10QA5 (Oryza sativa subsp. japonica)
Explore Q10QA5 
Go to UniProtKB:  Q10QA5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ10QA5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GR2
Query on GR2

Download Ideal Coordinates CCD File 
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 
IDSourceBinding 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 = 48.4α = 90
b = 87.88β = 90
c = 118.57γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesDK071662
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM102545
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM104212
National Natural Science Foundation of China (NSFC)ChinaNSFC 31300245
National Natural Science Foundation of China (NSFC)ChinaNSFC 91217311
Ministry of Science and Technology (MoST, China)China2012ZX09301001
Ministry of Science and Technology (MoST, China)China2012CB910403
Ministry of Science and Technology (MoST, China)China2013CB910600
Ministry of Science and Technology (MoST, China)ChinaXDB08020303
Ministry of Science and Technology (MoST, China)China2013ZX09507001

Revision History  (Full details and data files)

  • 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
  • Version 1.4: 2023-09-27
    Changes: Data collection, Database references, Refinement description