6BRT

F-box protein CTH with hydrolase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.248 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural plasticity of D3-D14 ubiquitin ligase in strigolactone signalling.

Shabek, N.Ticchiarelli, F.Mao, H.Hinds, T.R.Leyser, O.Zheng, N.

(2018) Nature 563: 652-656

  • DOI: https://doi.org/10.1038/s41586-018-0743-5
  • Primary Citation of Related Structures:  
    6BRO, 6BRP, 6BRQ, 6BRT

  • PubMed Abstract: 

    The strigolactones, a class of plant hormones, regulate many aspects of plant physiology. In the inhibition of shoot branching, the α/β hydrolase D14-which metabolizes strigolactone-interacts with the F-box protein D3 to ubiquitinate and degrade the transcription repressor D53. Despite the fact that multiple modes of interaction between D14 and strigolactone have recently been determined, how the hydrolase functions with D3 to mediate hormone-dependent D53 ubiquitination remains unknown. Here we show that D3 has a C-terminal α-helix that can switch between two conformational states. The engaged form of this α-helix facilitates the binding of D3 and D14 with a hydrolysed strigolactone intermediate, whereas the dislodged form can recognize unmodified D14 in an open conformation and inhibits its enzymatic activity. The D3 C-terminal α-helix enables D14 to recruit D53 in a strigolactone-dependent manner, which in turn activates the hydrolase. By revealing the structural plasticity of the SCF D3-D14 ubiquitin ligase, our results suggest a mechanism by which the E3 coordinates strigolactone signalling and metabolism.


  • Organizational Affiliation

    Department of Pharmacology, University of Washington, Seattle, WA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
D3-CTH-D14-D-ring
A, B, C, D, E
A, B, C, D, E, F, G, H
285Oryza glumipatulaMutation(s): 0 
UniProt
Find proteins for A0A0D9Z3K8 (Oryza glumipatula)
Explore A0A0D9Z3K8 
Go to UniProtKB:  A0A0D9Z3K8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0D9Z3K8
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
H3M
Query on H3M

Download Ideal Coordinates CCD File 
I [auth A](5R)-5-hydroxy-3-methylfuran-2(5H)-one
C5 H6 O3
HQIZYPQNJWENRT-SCSAIBSYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.248 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 183.843α = 90
b = 183.843β = 90
c = 153.662γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-21
    Type: Initial release
  • Version 1.1: 2018-12-05
    Changes: Data collection, Database references
  • Version 1.2: 2018-12-12
    Changes: Data collection, Database references
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references