7XDX

Crystal structure of a receptor like kinase from Arabidopsis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.184 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural and biochemical basis of Arabidopsis FERONIA receptor kinase-mediated early signaling initiation.

Kong, Y.Chen, J.Jiang, L.Chen, H.Shen, Y.Wang, L.Yan, Y.Zhou, H.Zheng, H.Yu, F.Ming, Z.

(2023) Plant Commun 4: 100559-100559

  • DOI: https://doi.org/10.1016/j.xplc.2023.100559
  • Primary Citation of Related Structures:  
    7XDV, 7XDW, 7XDX, 7XDY

  • PubMed Abstract: 

    Accumulating evidence indicates that early and essential events for receptor-like kinase (RLK) function involve both autophosphorylation and substrate phosphorylation. However, the structural and biochemical basis for these events is largely unclear. Here, we used RLK FERONIA (FER) as a model and crystallized its core kinase domain (FER-KD) and two FER-KD mutants (K565R, S525A) in complexes with ATP/ADP and Mg 2+ in the unphosphorylated state. Unphosphorylated FER-KD was found to adopt an unexpected active conformation in its crystal structure. Moreover, unphosphorylated FER-KD mutants with reduced (S525A) or no catalytic activity (K565R) also adopt similar active conformations. Biochemical studies revealed that FER-KD is a dual-specificity kinase, and its autophosphorylation is accomplished via an intermolecular mechanism. Further investigations confirmed that initiating substrate phosphorylation requires autophosphorylation of the activation segment on T696, S701, and Y704. This study reveals the structural and biochemical basis for the activation and regulatory mechanism of FER, providing a paradigm for the early steps in RLK signaling initiation.


  • Organizational Affiliation

    State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning 530004, P.R. China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Receptor-like protein kinase FERONIA
A, B
313Arabidopsis thalianaMutation(s): 0 
Gene Names: FERAAK1SIRSRNAt3g51550F26O13.190
EC: 2.7.11.1
UniProt
Find proteins for Q9SCZ4 (Arabidopsis thaliana)
Explore Q9SCZ4 
Go to UniProtKB:  Q9SCZ4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9SCZ4
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.184 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.67α = 90
b = 82.95β = 93.3
c = 61.94γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
DIALSdata reduction
DIALSdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31700052

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-29
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2023-11-29
    Changes: Refinement description