6INR

The crystal structure of phytoplasmal effector causing phyllody symptoms 1 (PHYL1)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.256 
  • R-Value Observed: 0.257 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural insights into the interaction between phytoplasmal effector causing phyllody 1 and MADS transcription factors.

Liao, Y.T.Lin, S.S.Lin, S.J.Sun, W.T.Shen, B.N.Cheng, H.P.Lin, C.P.Ko, T.P.Chen, Y.F.Wang, H.C.

(2019) Plant J 100: 706-719

  • DOI: https://doi.org/10.1111/tpj.14463
  • Primary Citation of Related Structures:  
    6INR

  • PubMed Abstract: 

    Phytoplasmas are bacterial plant pathogens which can induce severe symptoms including dwarfism, phyllody and virescence in an infected plant. Because phytoplasmas infect many important crops such as peanut and papaya they have caused serious agricultural losses. The phytoplasmal effector causing phyllody 1 (PHYL1) is an important phytoplasmal pathogenic factor which affects the biological function of MADS transcription factors by interacting with their K (keratin-like) domain, thus resulting in abnormal plant developments such as phyllody. Until now, lack of information on the structure of PHYL1 has prevented a detailed understanding of the binding mechanism between PHYL1 and the MADS transcription factors. Here, we present the crystal structure of PHYL1 from peanut witches'-broom phytoplasma (PHYL1 Pn WB ). This protein was found to fold into a unique α-helical hairpin with exposed hydrophobic residues on its surface that may play an important role in its biological function. Using proteomics approaches, we propose a binding mode of PHYL1 Pn WB with the K domain of the MADS transcription factor SEPALLATA3 (SEP3_K) and identify the residues of PHYL1 Pn WB that are important for this interaction. Furthermore, using surface plasmon resonance we measure the binding strength of PHYL1 Pn WB proteins to SEP3_K. Lastly, based on confocal images, we found that α-helix 2 of PHYL1 Pn WB plays an important role in PHYL1-mediated degradation of SEP3. Taken together, these results provide a structural understanding of the specific binding mechanism between PHYL1 Pn WB and SEP3_K.


  • Organizational Affiliation

    The PhD Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11529, Taiwan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative effector, AYWB SAP54-like protein
A, B
93Candidatus Phytoplasma australasiaticum subsp. taiwanenseMutation(s): 0 
Gene Names: EPWB_v1c1980
UniProt
Find proteins for A0A0P7KHL3 ('Echinacea purpurea' witches'-broom phytoplasma)
Explore A0A0P7KHL3 
Go to UniProtKB:  A0A0P7KHL3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0P7KHL3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.256 
  • R-Value Observed: 0.257 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.006α = 90
b = 65.006β = 90
c = 193.432γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
Blu-Icedata collection
BUCCANEERmodel building
HKL-2000data reduction
SHELXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (Taiwan)Taiwan107-2313-B-038-001
Ministry of Science and Technology (Taiwan)TaiwanMOST106-2311-B-038-002
Ministry of Science and Technology (Taiwan)TaiwanNSC103-2311-B-038-005-MY3

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-31
    Type: Initial release
  • Version 1.1: 2019-09-25
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-27
    Changes: Database references
  • Version 1.3: 2024-03-27
    Changes: Data collection, Database references, Derived calculations, Refinement description