6A5E

Crystal structure of plant peptide RALF23 in complex with FER and LLG2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.77 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.235 

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This is version 2.1 of the entry. See complete history


Literature

Mechanisms of RALF peptide perception by a heterotypic receptor complex.

Xiao, Y.Stegmann, M.Han, Z.DeFalco, T.A.Parys, K.Xu, L.Belkhadir, Y.Zipfel, C.Chai, J.

(2019) Nature 572: 270-274

  • DOI: https://doi.org/10.1038/s41586-019-1409-7
  • Primary Citation of Related Structures:  
    6A5A, 6A5B, 6A5C, 6A5D, 6A5E

  • PubMed Abstract: 

    Receptor kinases of the Catharanthus roseus RLK1-like (CrRLK1L) family have emerged as important regulators of plant reproduction, growth and responses to the environment 1 . Endogenous RAPID ALKALINIZATION FACTOR (RALF) peptides 2 have previously been proposed as ligands for several members of the CrRLK1L family 1 . However, the mechanistic basis of this perception is unknown. Here we report that RALF23 induces a complex between the CrRLK1L FERONIA (FER) and LORELEI (LRE)-LIKE GLYCOSYLPHOSPHATIDYLINOSITOL (GPI)-ANCHORED PROTEIN 1 (LLG1) to regulate immune signalling. Structural and biochemical data indicate that LLG1 (which is genetically important for RALF23 responses) and the related LLG2 directly bind RALF23 to nucleate the assembly of RALF23-LLG1-FER and RALF23-LLG2-FER heterocomplexes, respectively. A conserved N-terminal region of RALF23 is sufficient for the biochemical recognition of RALF23 by LLG1, LLG2 or LLG3, and binding assays suggest that other RALF peptides that share this conserved N-terminal region may be perceived by LLG proteins in a similar manner. Structural data also show that RALF23 recognition is governed by the conformationally flexible C-terminal sides of LLG1, LLG2 and LLG3. Our work reveals a mechanism of peptide perception in plants by GPI-anchored proteins that act together with a phylogenetically unrelated receptor kinase. This provides a molecular framework for understanding how diverse RALF peptides may regulate multiple processes, through perception by distinct heterocomplexes of CrRLK1L receptor kinases and GPI-anchored proteins of the LRE and LLG family.


  • Organizational Affiliation

    School of Life Sciences, Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Receptor-like protein kinase FERONIAA,
F [auth B]
396Arabidopsis thalianaMutation(s): 0 
Gene Names: FER
EC: 2.7.11.1
UniProt
Find proteins for Q9SCZ4 (Arabidopsis thaliana)
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Go to UniProtKB:  Q9SCZ4
Entity Groups  
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UniProt GroupQ9SCZ4
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
GPI-anchored protein LLG2B [auth C],
E [auth D]
84Arabidopsis thalianaMutation(s): 0 
Gene Names: LLG2At2g20700
UniProt
Find proteins for Q6NLF4 (Arabidopsis thaliana)
Explore Q6NLF4 
Go to UniProtKB:  Q6NLF4
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UniProt GroupQ6NLF4
Glycosylation
Glycosylation Sites: 1
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
RALF23C [auth E],
D [auth F]
15ArabidopsisMutation(s): 0 
UniProt
Find proteins for Q9LUS7 (Arabidopsis thaliana)
Explore Q9LUS7 
Go to UniProtKB:  Q9LUS7
Entity Groups  
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UniProt GroupQ9LUS7
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
G, H, I, J
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.77 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.235 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.312α = 105.72
b = 62.36β = 91.3
c = 97.478γ = 108.48
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-26
    Type: Initial release
  • Version 1.1: 2020-01-15
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-11-13
    Changes: Data collection, Database references, Structure summary