9H6V | pdb_00009h6v

Lotus japonicus CERK6 extracellular domain in complex with two nanobodies

• PDB DOI: https://doi.org/10.2210/pdb9H6V/pdb

• Classification: PLANT PROTEIN
• Organism(s): Lotus japonicus, Lama glama
• Expression System: Spodoptera frugiperda, Escherichia coli
• Mutation(s): No 


• Deposited: 2024-10-25 Released: 2025-07-16 
• Deposition Author(s): Gysel, K., Alsarraf, H.M.A.B., Hansen, S.B., Andersen, K.R.
• Funding Organization(s): The Carlsberg Foundation, Danish Agency for Science Technology and Innovation, Novo Nordisk Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free: 
  0.252 (Depositor), 0.253 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.204 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Models: experimental

Literature

Structural basis for size-selective perception of chitin in plants

Gysel, K., Hansen, S.B., Ruebsam, H., Alsarraf, H.M.A.B., Madland, E., Cheng, J.X.J., Baadegaard, C., Poulsen, E.C., Vinther, M., Fort, S., Stougaard, J., Andersen, K.R.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 107.04 kDa 
• Atom Count: 7,128 
• Modeled Residue Count: 883 
• Deposited Residue Count: 940 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LysM type receptor kinase	A, B	204	Lotus japonicus	Mutation(s): 0  Gene Names: LYS6 EC: 2.7.11.1
UniProt
Find proteins for D3KTZ6 (Lotus japonicus) Explore D3KTZ6  Go to UniProtKB:  D3KTZ6
Glycosylation
Glycosylation Sites: 4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nb-aCERK6-2	C [auth E], D [auth F]	133	Lama glama	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Nb-aCERK6-1	E [auth D], F [auth C]	133	Lama glama	Mutation(s): 0

Oligosaccharides

Help  

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G, H, I	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	J [auth A], K [auth A], M [auth B], N [auth B], P [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
EDO	L [auth A], O [auth B], Q [auth E], R [auth F], S [auth D], T [auth D], U [auth D], V [auth C], W [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free:  0.252 (Depositor), 0.253 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.204 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.28	α = 96.972
b = 57.58	β = 88.981
c = 86.81	γ = 96.418

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
STARANISO	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-07-16 
Deposition Author(s): Gysel, K., Alsarraf, H.M.A.B., Hansen, S.B., Andersen, K.R.

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Funding Organization	Location	Grant Number
The Carlsberg Foundation	Denmark	CF21-0139
Danish Agency for Science Technology and Innovation	Denmark	3103-00137B
Novo Nordisk Foundation	Denmark	NNF21OC0071300

Revision History  

• Version 1.0: 2025-07-16
  Type: Initial release