8YAA | pdb_00008yaa

Cryo-EM structure of MIK2-SCOOP12-BAK1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.34 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

N-glycosylation facilitates the activation of a plant cell-surface receptor.

Jia, F.Xiao, Y.Feng, Y.Yan, J.Fan, M.Sun, Y.Huang, S.Li, W.Zhao, T.Han, Z.Hou, S.Chai, J.

(2024) Nat Plants 10: 2014-2026

  • DOI: https://doi.org/10.1038/s41477-024-01841-6
  • Primary Citation of Related Structures:  
    8YAA

  • PubMed Abstract: 

    Plant receptor kinases (RKs) are critical for transmembrane signalling involved in various biological processes including plant immunity. MALE DISCOVERER1-INTERACTING RECEPTOR-LIKE KINASE 2 (MIK2) is a unique RK that recognizes a family of immunomodulatory peptides called SERINE-RICH ENDOGENOUS PEPTIDEs (SCOOPs) and activates pattern-triggered immunity responses. However, the precise mechanisms underlying SCOOP recognition and activation of MIK2 remain poorly understood. Here we present the cryogenic electron microscopy structure of a ternary complex consisting of the extracellular leucine-rich repeat (LRR) of MIK2 (MIK2LRR), SCOOP12 and the extracellular LRR of the co-receptor BAK1 (BAK1LRR) at a resolution of 3.34 Å. The structure reveals that a DNHH motif in MIK2LRR plays a critical role in specifically recognizing the highly conserved SxS motif of SCOOP12. Furthermore, the structure demonstrates that N-glycans at MIK2LRR Asn410 directly interact with the N-terminal capping region of BAK1LRR. Mutation of the glycosylation site, MIK2LRR N410D , completely abolishes the SCOOP12-independent interaction between MIK2LRR and BAK1LRR and substantially impairs the assembly of the MIK2LRR-SCOOP12-BAK1LRR complex. Supporting the biological relevance of N410-glycosylation, MIK2 N410D substantially compromises SCOOP12-triggered immune responses in plants. Collectively, these findings elucidate the mechanism underlying the loose specificity of SCOOP recognition by MIK2 and reveal an unprecedented mechanism by which N-glycosylation modification of LRR-RK promotes receptor activation.


  • Organizational Affiliation

    College of Life Sciences, Henan Normal University, Xinxiang, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1A [auth C]177Arabidopsis 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
Glycosylation
Glycosylation Sites: 4
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
MDIS1-interacting receptor like kinase 2B [auth A]654Arabidopsis thalianaMutation(s): 0 
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: 16
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Serine rich endogenous peptide 12C [auth B]13Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for B3H7I1 (Arabidopsis thaliana)
Explore B3H7I1 
Go to UniProtKB:  B3H7I1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB3H7I1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D
5N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO
GlyCosmos:  G22768VO
GlyGen:  G22768VO
Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E, F, G, H, J
E, F, G, H, J, K, L, M, N, O
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 6
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
I
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.34 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-30
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Data collection
  • Version 1.2: 2024-11-20
    Changes: Data collection, Database references
  • Version 1.3: 2024-11-27
    Changes: Data collection, Database references
  • Version 1.4: 2025-01-01
    Changes: Data collection, Database references