6BRQ

Crystal structure of rice ASK1-D3 ubiquitin ligase complex crystal form 3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.220 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: 10.1038/s41586-018-0743-5
  • Primary Citation of Related Structures:  
    6BRO, 6BRQ, 6BRP, 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 ...

    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

    Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA. nzheng@uw.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
F-box/LRR-repeat MAX2 homologA [auth B], C [auth D]688Oryza sativa Japonica GroupMutation(s): 0 
Gene Names: D3Os06g0154200LOC_Os06g06050OSJNBa0085L11.6-1
UniProt
Find proteins for Q5VMP0 (Oryza sativa subsp. japonica)
Explore Q5VMP0 
Go to UniProtKB:  Q5VMP0
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
SKP1-like protein 1AB [auth A], D [auth C]160Arabidopsis thalianaMutation(s): 0 
Gene Names: SKP1AASK1SKP1UIP1At1g75950T4O12.17
UniProt
Find proteins for Q39255 (Arabidopsis thaliana)
Explore Q39255 
Go to UniProtKB:  Q39255
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.220 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.908α = 90
b = 113.306β = 99
c = 92.858γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
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