8WEC

Crystal structure of Arabidopsis thaliana MIK2 ectodomain in complex with BAK1 ectodomain and SCOOP12


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.245 

Starting Model: in silico
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Mechanistic study of SCOOPs recognition by MIK2-BAK1 complex reveals the role of N-glycans in plant ligand-receptor-coreceptor complex formation.

Wu, H.Wan, L.Liu, Z.Jian, Y.Zhang, C.Mao, X.Wang, Z.Wang, Q.Hu, Y.Xiong, L.Xia, Z.Xue, J.Li, S.He, P.Shan, L.Xu, S.

(2024) Nat Plants 10: 1984-1998

  • DOI: https://doi.org/10.1038/s41477-024-01836-3
  • Primary Citation of Related Structures:  
    8WEB, 8WEC, 8WED, 8WEE, 8WEF, 8WEG, 8WEH, 8WEI

  • PubMed Abstract: 

    Ligand-induced receptor and co-receptor heterodimerization is a common mechanism in receptor kinase (RK) signalling activation. SERINE-RICH ENDOGENOUS PEPTIDEs (SCOOPs) mediate the complex formation of Arabidopsis RK MIK2 and co-receptor BAK1, triggering immune responses. Through structural, biochemical and genetic analyses, we demonstrate that SCOOPs use their SxS motif and adjacent residues to bind MIK2 and the carboxy-terminal GGR residues to link MIK2 to BAK1. While N-glycosylation of plant RKs is typically associated with protein maturation, plasma membrane targeting and conformation maintenance, a surprising revelation emerges from our crystal structural analysis of MIK2-SCOOP-BAK1 complexes. Specific N-glycans on MIK2 directly interact with BAK1 upon SCOOP sensing. The absence of N-glycosylation at the specific site in MIK2 neither affects its subcellular localization and protein accumulation in plant cells nor alters its structural conformation, but markedly reduces its affinity for BAK1, abolishing SCOOP-triggered immune responses. This N-glycan-mediated receptor and co-receptor heterodimerization occurs in both Arabidopsis and Brassica napus. Our findings elucidate the molecular basis of SCOOP perception by the MIK2-BAK1 immune complex and underscore the crucial role of N-glycans in plant receptor-coreceptor interactions and signalling activation, shaping immune responses.


  • Organizational Affiliation

    National Key Lab of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MDIS1-interacting receptor like kinase 2
A, D
683Arabidopsis thalianaMutation(s): 3 
Gene Names: MIK2At4g08850T32A17.160
EC: 2.7.11.1
UniProt
Find proteins for Q8VZG8 (Arabidopsis thaliana)
Explore Q8VZG8 
Go to UniProtKB:  Q8VZG8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8VZG8
Glycosylation
Glycosylation Sites: 10
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1
B, E
230Arabidopsis thalianaMutation(s): 0 
Gene Names: BAK1ELGSERK3At4g33430F17M5.190
EC: 2.7.10.1 (PDB Primary Data), 2.7.11.1 (PDB Primary Data)
UniProt
Find proteins for Q94F62 (Arabidopsis thaliana)
Explore Q94F62 
Go to UniProtKB:  Q94F62
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ94F62
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
SERINE-RICH ENDOGENOUS PEPTIDE (SCOOP)
C, F
13Arabidopsis thalianaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
G, I, J, K, L
G, I, J, K, L, Q, R, S, W
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
H
4N-Glycosylation
Glycosylation Resources
GlyTouCan:  G63564LA
GlyCosmos:  G63564LA
Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
M, O
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB
GlyCosmos:  G21290RB
GlyGen:  G21290RB
Entity ID: 7
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
N, T
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 8
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose
P
2N/A
Glycosylation Resources
GlyTouCan:  G07696MJ
GlyCosmos:  G07696MJ
GlyGen:  G07696MJ
Entity ID: 9
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose
U, V
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G86851RC
GlyCosmos:  G86851RC
GlyGen:  G86851RC
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
BA [auth D]
CA [auth D]
DA [auth D]
EA [auth D]
FA [auth D]
BA [auth D],
CA [auth D],
DA [auth D],
EA [auth D],
FA [auth D],
X [auth A],
Y [auth A],
Z [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
BMA (Subject of Investigation/LOI)
Query on BMA

Download Ideal Coordinates CCD File 
AA [auth B]beta-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.245 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.004α = 90
b = 178.69β = 90.79
c = 144.161γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32000900

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-06
    Type: Initial release
  • Version 1.1: 2024-11-27
    Changes: Database references
  • Version 1.2: 2024-12-25
    Changes: Database references