7VS7

Crystal structure of the ectodomain of OsCERK1 in complex with chitin hexamer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural insight into chitin perception by chitin elicitor receptor kinase 1 of Oryza sativa.

Xu, L.Wang, J.Xiao, Y.Han, Z.Chai, J.

(2023) J Integr Plant Biol 65: 235-248

  • DOI: https://doi.org/10.1111/jipb.13279
  • Primary Citation of Related Structures:  
    7VS7

  • PubMed Abstract: 

    Plants have developed innate immune systems to fight against pathogenic fungi by monitoring pathogenic signals known as pathogen-associated molecular patterns (PAMP) and have established endo symbiosis with arbuscular mycorrhizal (AM) fungi through recognition of mycorrhizal (Myc) factors. Chitin elicitor receptor kinase 1 of Oryza sativa subsp. Japonica (OsCERK1) plays a bifunctional role in mediating both chitin-triggered immunity and symbiotic relationships with AM fungi. However, it remains unclear whether OsCERK1 can directly recognize chitin molecules. In this study, we show that OsCERK1 binds to the chitin hexamer ((NAG) 6 ) and tetramer ((NAG) 4 ) directly and determine the crystal structure of the OsCERK1-(NAG) 6 complex at 2 Å. The structure shows that one OsCERK1 is associated with one (NAG) 6 . Upon recognition, chitin hexamer binds OsCERK1 by interacting with the shallow groove on the surface of LysM2. These structural findings, complemented by mutational analyses, demonstrate that LysM2 is crucial for recognition of both (NAG) 6 and (NAG) 4 . Altogether, these findings provide structural insights into the ability of OsCERK1 in chitin perception, which will lead to a better understanding of the role of OsCERK1 in mediating both immunity and symbiosis in rice.


  • Organizational Affiliation

    Tsinghua-Peking Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Centre for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chitin elicitor receptor kinase 1217Oryza sativa Japonica GroupMutation(s): 0 
Gene Names: CERK1RLK9Os08g0538300LOC_Os08g42580P0665C04.34P0666G10.101
EC: 2.7.11.1
UniProt
Find proteins for A0A0P0XII1 (Oryza sativa subsp. japonica)
Explore A0A0P0XII1 
Go to UniProtKB:  A0A0P0XII1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0P0XII1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D 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
B
6N/A
Glycosylation Resources
GlyTouCan:  G36414FS
GlyCosmos:  G36414FS
GlyGen:  G36414FS
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
C
5N-Glycosylation
Glycosylation Resources
GlyTouCan:  G92953ND
GlyCosmos:  G92953ND
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D, E
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.043α = 90
b = 61.406β = 113.65
c = 46.409γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Released Date: 2022-08-03 
  • Deposition Author(s): Li, X.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-03
    Type: Initial release
  • Version 1.1: 2023-02-15
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description