6A5E | pdb_00006a5e

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 (Depositor), 0.300 (DCC) 
  • R-Value Work: 
    0.233 (Depositor), 0.264 (DCC) 
  • R-Value Observed: 
    0.235 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

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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  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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
Sequence Annotations
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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 (Depositor), 0.300 (DCC) 
  • R-Value Work:  0.233 (Depositor), 0.264 (DCC) 
  • R-Value Observed: 0.235 (Depositor) 
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 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NAGClick on this verticalbar to view details

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