9GB9 | pdb_00009gb9

Crystal structure of Lotus japonicus CERK6 kinase domain D460N


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 
    0.242 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.209 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 
    0.210 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Two residues reprogram immunity receptors for nitrogen-fixing symbiosis.

Tsitsikli, M.Simonsen, B.Luu, T.B.Larsen, M.M.Andersen, C.G.Gysel, K.Lironi, D.Kronauer, C.Rubsam, H.Hansen, S.B.Baerentsen, R.Wulff, J.L.Johansen, S.H.Sezer, G.Stougaard, J.Andersen, K.R.Radutoiu, S.

(2025) Nature 

  • DOI: https://doi.org/10.1038/s41586-025-09696-3
  • Primary Citation of Related Structures:  
    9GB9, 9GFZ

  • PubMed Abstract: 

    Receptor signalling determines cellular responses and is crucial for defining specific biological outcomes. In legume root cells, highly similar and structurally conserved chitin and Nod factor receptor kinases activate immune or symbiotic pathways, respectively, when chitinous ligands are perceived 1 . Here we show that specific amino acid residues in the intracellular part of the Nod factor receptor NFR1 control signalling specificity and enable the distinction of immune and symbiotic responses. Functional investigation of CERK6, NFR1 and receptor variants thereof revealed a conserved motif that we term Symbiosis Determinant 1 in the juxtamembrane region of the kinase domain, which is key for symbiotic signalling. We show that two residues in Symbiosis Determinant 1 are indispensable hallmarks of NFR1-type receptors and are sufficient to convert Lotus CERK6 and barley RLK4 kinase outputs to enable symbiotic signalling in Lotus japonicus.


  • Organizational Affiliation
    • Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LysM type receptor kinase
A, B, C, D
297Lotus japonicusMutation(s): 1 
Gene Names: LYS6
EC: 2.7.11.1
UniProt
Find proteins for D3KTZ6 (Lotus japonicus)
Explore D3KTZ6 
Go to UniProtKB:  D3KTZ6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD3KTZ6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IMD
Query on IMD

Download Ideal Coordinates CCD File 
L [auth B],
T [auth C]
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
EDO
Query on EDO

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth B]
H [auth B]
I [auth B]
E [auth A],
F [auth A],
G [auth B],
H [auth B],
I [auth B],
J [auth B],
K [auth B],
M [auth B],
N [auth C],
O [auth C],
P [auth C],
Q [auth C],
R [auth C],
S [auth C],
U [auth C],
V [auth C],
W [auth D],
X [auth D],
Y [auth D],
Z [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free:  0.242 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.209 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 0.210 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.92α = 106.457
b = 59.99β = 97.306
c = 103.74γ = 106.638
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Novo Nordisk FoundationDenmarkNNF18OC0052855

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-27
    Type: Initial release
  • Version 1.1: 2025-03-26
    Changes: Structure summary
  • Version 1.2: 2025-07-16
    Changes: Database references
  • Version 1.3: 2025-12-10
    Changes: Database references