6A5A | pdb_00006a5a

Crystal structure of plant Receptor-like Kinase ANX1

• PDB DOI: https://doi.org/10.2210/pdb6A5A/pdb

• Classification: TRANSFERASE
• Organism(s): Arabidopsis thaliana
• Expression System: Insect cell expression vector pTIE1
• Mutation(s): No 


• Deposited: 2018-06-22 Released: 2019-06-26 
• Deposition Author(s): Xiao, Y., Chai, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.94 Å
• R-Value Free: 
  0.260 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.223 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: experimental

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

• PubMed: 31291642 
• DOI: https://doi.org/10.1038/s41586-019-1409-7
• Primary Citation 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.

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Organizational Affiliation: 
• School of Life Sciences, Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China.
The Sainsbury Laboratory, University of East Anglia, Norwich, UK.
Department of Phytopathology, Technical University of Munich, School of Life Sciences Weihenstephan, Freising, Germany.
Institute of Plant and Microbial Biology, Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland.
Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria.
The Sainsbury Laboratory, University of East Anglia, Norwich, UK. [e-mail].
Institute of Plant and Microbial Biology, Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland. [e-mail].
School of Life Sciences, Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China. [e-mail].
Max-Planck Institute for Plant Breeding Research, Cologne, Germany. [e-mail].
Institute of Biochemistry, University of Cologne, Cologne, Germany. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 85.79 kDa 
• Atom Count: 5,920 
• Modeled Residue Count: 752 
• Deposited Residue Count: 770 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Receptor-like protein kinase ANXUR1	A [auth B], B [auth A]	385	Arabidopsis thaliana	Mutation(s): 0  Gene Names: ANX1 EC: 2.7.11.1
UniProt
Find proteins for Q9SR05 (Arabidopsis thaliana) Explore Q9SR05  Go to UniProtKB:  Q9SR05

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.94 Å
• R-Value Free:  0.260 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.223 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.337	α = 90
b = 77.546	β = 100.52
c = 99.288	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-06-26 
Deposition Author(s): Xiao, Y., Chai, J.

Revision History  

• Version 1.0: 2019-06-26
  Type: Initial release
  
• Version 1.1: 2020-01-15
  Changes: Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description