9H3A | pdb_00009h3a

Crystal structure of Lotus japonicus CHIP13 extracellular domain in complex with chitooctaose

• PDB DOI: https://doi.org/10.2210/pdb9H3A/pdb

• Classification: PLANT PROTEIN
• Organism(s): Lotus japonicus
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2024-10-16 Released: 2025-07-16 
• Deposition Author(s): Gysel, K., Andersen, K.R.
• Funding Organization(s): The Carlsberg Foundation, Danish Council for Independent Research, Novo Nordisk Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 
  0.191 (Depositor), 0.191 (DCC) 
• R-Value Work: 
  0.153 (Depositor), 0.153 (DCC) 
• R-Value Observed: 
  0.155 (Depositor) 

Starting Model: 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: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: mass spectrometry, gel filtration

Macromolecule Content 

• Total Structure Weight: 27.81 kDa 
• Atom Count: 2,386 
• Modeled Residue Count: 227 
• Deposited Residue Count: 227 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LysM type receptor kinase	A	227	Lotus japonicus	Mutation(s): 0  Gene Names: LYS13
UniProt
Find proteins for D3KU00 (Lotus japonicus) Explore D3KU00  Go to UniProtKB:  D3KU00
Glycosylation
Glycosylation Sites: 3

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	8		N/A
Glycosylation Resources
GlyTouCan:  G83257UC GlyCosmos:  G83257UC

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D	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 (Subject of Investigation/LOI)	F [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA	A	L-PEPTIDE LINKING	C5 H7 N O3		GLN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free:  0.191 (Depositor), 0.191 (DCC) 
• R-Value Work:  0.153 (Depositor), 0.153 (DCC) 
• R-Value Observed: 0.155 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.75	α = 90
b = 45.55	β = 102.261
c = 75.56	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-16 
Deposition Author(s): Gysel, K., Andersen, K.R.

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Funding Organization	Location	Grant Number
The Carlsberg Foundation	Denmark	CF21-0139
Danish Council for Independent Research	Denmark	3103-00137B
Novo Nordisk Foundation	Denmark	NNF21OC0071300

Revision History  

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