9H39 | pdb_00009h39

Crystal structure of Lotus japonicus CHIP13 extracellular domain in complex with a nanobody

• PDB DOI: https://doi.org/10.2210/pdb9H39/pdb

• Classification: PLANT PROTEIN
• Organism(s): Lotus japonicus, Lama glama
• Expression System: Spodoptera frugiperda, Escherichia coli
• 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: 1.66 Å
• R-Value Free: 
  0.225 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.183 (DCC) 
• R-Value Observed: 
  0.183 (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 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 82.21 kDa 
• Atom Count: 6,190 
• Modeled Residue Count: 679 
• Deposited Residue Count: 710 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LysM type receptor kinase	A, B	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
anti-LYS13 VHH	C, D	128	Lama glama	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E [auth N]	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F [auth E], G [auth M]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	H [auth F]	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G32152BH GlyCosmos:  G32152BH GlyGen:  G32152BH

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	I [auth G]	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB GlyCosmos:  G21290RB GlyGen:  G21290RB

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	J [auth B], K [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free:  0.225 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.183 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.9	α = 90
b = 55.09	β = 98.91
c = 109.34	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