Biological Assembly 1  

 3D View: Structure | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 25.54 kDa 
• Atom Count: 2031 
• Modelled Residue Count: 200 
• Deposited Residue Count: 212 
• Unique protein chains: 1

4EBY

Crystal structure of the ectodomain of a receptor like kinase

• DOI: 10.2210/pdb4EBY/pdb

• Classification: TRANSFERASE
• Organism(s): Arabidopsis thaliana
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2012-03-25 Released: 2012-06-27 
• Deposition Author(s): Chai, J., Liu, T., Han, Z., She, J, Wang, J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.189 
• R-Value Work: 0.171 
• R-Value Observed: 0.172 

Literature

Chitin-induced dimerization activates a plant immune receptor.

Liu, T., Liu, Z., Song, C., Hu, Y., Han, Z., She, J., Fan, F., Wang, J., Jin, C., Chang, J., Zhou, J.M., Chai, J.

(2012) Science 336: 1160-1164

• PubMed: 22654057 
• DOI: 10.1126/science.1218867
• Primary Citation of Related Structures:  
  4EBY, 4EBZ


• PubMed Abstract: 
  

Pattern recognition receptors confer plant resistance to pathogen infection by recognizing the conserved pathogen-associated molecular patterns. The cell surface receptor chitin elicitor receptor kinase 1 of Arabidopsis (AtCERK1) directly binds chitin through its lysine motif (LysM)-containing ectodomain (AtCERK1-ECD) to activate immune responses. The crystal structure that we solved of an AtCERK1-ECD complexed with a chitin pentamer reveals that their interaction is primarily mediated by a LysM and three chitin residues. By acting as a bivalent ligand, a chitin octamer induces AtCERK1-ECD dimerization that is inhibited by shorter chitin oligomers. A mutation attenuating chitin-induced AtCERK1-ECD dimerization or formation of nonproductive AtCERK1 dimer by overexpression of AtCERK1-ECD compromises AtCERK1-mediated signaling in plant cells. Together, our data support the notion that chitin-induced AtCERK1 dimerization is critical for its activation.

---

Organizational Affiliation: 

Graduate Program in Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chitin elicitor receptor kinase 1	A	212	Arabidopsis thaliana	Mutation(s): 0  Gene Names: CERK1, At3g21630, LYK1, RLK1, MIL23.20 EC: 2.7.11.1
UniProt
Find proteins for A8R7E6 (Arabidopsis thaliana) Explore A8R7E6  Go to UniProtKB:  A8R7E6

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B, C, D	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

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

Small Molecules

Ligands 1 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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.189 
• R-Value Work: 0.171 
• R-Value Observed: 0.172 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.829	α = 90
b = 71.128	β = 90
c = 72.761	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SHELXS	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2012-03-25 
• Released Date: 2012-06-27 
Deposition Author(s): Chai, J., Liu, T., Han, Z., She, J, Wang, J.

Revision History  

• Version 1.0: 2012-06-27
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary