5Y9W

Crystal 1 for AtLURE1.2-AtPRK6LRR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis for receptor recognition of pollen tube attraction peptides.

Zhang, X.Liu, W.Nagae, T.T.Takeuchi, H.Zhang, H.Han, Z.Higashiyama, T.Chai, J.

(2017) Nat Commun 8: 1331-1331

  • DOI: https://doi.org/10.1038/s41467-017-01323-8
  • Primary Citation of Related Structures:  
    5Y9W, 5YAH

  • PubMed Abstract: 

    Transportation of the immobile sperms directed by pollen tubes to the ovule-enclosed female gametophytes is important for plant sexual reproduction. The defensin-like (DEFL) cysteine-rich peptides (CRPs) LUREs play an essential role in pollen tube attraction to the ovule, though their receptors still remain controversial. Here we provide several lines of biochemical evidence showing that the extracellular domain of the leucine-rich repeat receptor kinase (LRR-RK) PRK6 from Arabidopsis thaliana directly interacts with AtLURE1 peptides. Structural study reveals that a C-terminal loop of the LRR domain (AtPRK6 LRR ) is responsible for recognition of AtLURE1.2, mediated by a set of residues largely conserved among PRK6 homologs from Arabidopsis lyrata and Capsella rubella, supported by in vitro mutagenesis and semi-in-vivo pollen tube growth assays. Our study provides evidence showing that PRK6 functions as a receptor of the LURE peptides in A. thaliana and reveals a unique ligand recognition mechanism of LRR-RKs.


  • Organizational Affiliation

    Ministry of Education Key Laboratory of Protein Science, Center for Structural Biology, School of Life Sciences, Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, 100084, Beijing, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pollen receptor-like kinase 6A [auth B],
C [auth A]
242Arabidopsis thalianaMutation(s): 0 
Gene Names: PRK6At5g20690T1M15.90
UniProt
Find proteins for Q3E991 (Arabidopsis thaliana)
Explore Q3E991 
Go to UniProtKB:  Q3E991
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3E991
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protein LURE 1.2B [auth C]71Arabidopsis thalianaMutation(s): 0 
Gene Names: LURE1.2CRP810_1.2At5g43510MWF20.23
UniProt
Find proteins for Q4VP08 (Arabidopsis thaliana)
Explore Q4VP08 
Go to UniProtKB:  Q4VP08
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4VP08
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.687α = 90
b = 48.511β = 102.67
c = 146.31γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Blu-Icedata collection
HKL-3000data scaling
PHASERphasing
HKL-3000data reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-27
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description