8T2I

Negative stain EM assembly of MYC, JAZ, and NINJA complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 10.4 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Assembly of JAZ-JAZ and JAZ-NINJA complexes in jasmonate signaling.

Zhou, X.E.Zhang, Y.Yao, J.Zheng, J.Zhou, Y.He, Q.Moreno, J.Lam, V.Q.Cao, X.Sugimoto, K.Vanegas-Cano, L.Kariapper, L.Suino-Powell, K.Zhu, Y.Novick, S.Griffin, P.R.Zhang, F.Howe, G.A.Melcher, K.

(2023) Plant Commun 4: 100639-100639

  • DOI: https://doi.org/10.1016/j.xplc.2023.100639
  • Primary Citation of Related Structures:  
    8T2I

  • PubMed Abstract: 

    Jasmonates (JAs) are plant hormones with crucial roles in development and stress resilience. They activate MYC transcription factors by mediating the proteolysis of MYC inhibitors called JAZ proteins. In the absence of JA, JAZ proteins bind and inhibit MYC through the assembly of MYC-JAZ-Novel Interactor of JAZ (NINJA)-TPL repressor complexes. However, JAZ and NINJA are predicted to be largely intrinsically unstructured, which has precluded their experimental structure determination. Through a combination of biochemical, mutational, and biophysical analyses and AlphaFold-derived ColabFold modeling, we characterized JAZ-JAZ and JAZ-NINJA interactions and generated models with detailed, high-confidence domain interfaces. We demonstrate that JAZ, NINJA, and MYC interface domains are dynamic in isolation and become stabilized in a stepwise order upon complex assembly. By contrast, most JAZ and NINJA regions outside of the interfaces remain highly dynamic and cannot be modeled in a single conformation. Our data indicate that the small JAZ Zinc finger expressed in Inflorescence Meristem (ZIM) motif mediates JAZ-JAZ and JAZ-NINJA interactions through separate surfaces, and our data further suggest that NINJA modulates JAZ dimerization. This study advances our understanding of JA signaling by providing insights into the dynamics, interactions, and structure of the JAZ-NINJA core of the JA repressor complex.


  • Organizational Affiliation

    Department of Structural Biology, Van Andel Institute, Grand Rapids, MI 49503, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription factor MYC3190Arabidopsis thalianaMutation(s): 0 
Gene Names: MYC3ATR2BHLH5EN36At5g46760MZA15.18
UniProt
Find proteins for Q9FIP9 (Arabidopsis thaliana)
Explore Q9FIP9 
Go to UniProtKB:  Q9FIP9
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9FIP9
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Maltose/maltodextrin-binding periplasmic proteinB [auth M]404Escherichia coliMutation(s): 0 
Gene Names: malEZ5632ECs5017
UniProt
Find proteins for P0AEX9 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0AEX9
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UniProt GroupP0AEX9
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Protein TIFY 10AC [auth J]253Arabidopsis thalianaMutation(s): 0 
Gene Names: TIFY10AJAZ1At1g19180T29M8.5
UniProt
Find proteins for Q9LMA8 (Arabidopsis thaliana)
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Go to UniProtKB:  Q9LMA8
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UniProt GroupQ9LMA8
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
AFP homolog 2D [auth N]425Arabidopsis thalianaMutation(s): 0 
Gene Names: AFPH2NINJAAt4g28910F25O24.30
UniProt
Find proteins for Q9SV55 (Arabidopsis thaliana)
Explore Q9SV55 
Go to UniProtKB:  Q9SV55
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UniProt GroupQ9SV55
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 10.4 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United States1922846

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-28
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references