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- PDB-8t2i: Negative stain EM assembly of MYC, JAZ, and NINJA complex -

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Basic information

Entry
Database: PDB / ID: 8t2i
TitleNegative stain EM assembly of MYC, JAZ, and NINJA complex
Components
  • AFP homolog 2
  • Maltose/maltodextrin-binding periplasmic protein
  • Protein TIFY 10A
  • Transcription factor MYC3
KeywordsSIGNALING PROTEIN / Jasmonate signaling / MYC / JAZ / NINJA
Function / homology
Function and homology information


regulation of cellular response to alkaline pH / regulation of leaf morphogenesis / extracellular ATP signaling / anthocyanin-containing compound biosynthetic process / stomatal complex development / jasmonic acid mediated signaling pathway / flower development / bHLH transcription factor binding / pollen development / response to jasmonic acid ...regulation of cellular response to alkaline pH / regulation of leaf morphogenesis / extracellular ATP signaling / anthocyanin-containing compound biosynthetic process / stomatal complex development / jasmonic acid mediated signaling pathway / flower development / bHLH transcription factor binding / pollen development / response to jasmonic acid / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / defense response / outer membrane-bounded periplasmic space / protein dimerization activity / defense response to bacterium / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / DNA binding / identical protein binding / nucleus / plasma membrane
Similarity search - Function
Ninja family / Tify domain binding domain / Tify domain binding domain / Tify domain / CO/COL/TOC1, conserved site / TIFY/JAZ family / tify domain / Jas motif / Tify domain profile. / TIFY ...Ninja family / Tify domain binding domain / Tify domain binding domain / Tify domain / CO/COL/TOC1, conserved site / TIFY/JAZ family / tify domain / Jas motif / Tify domain profile. / TIFY / Transcription factor AIB/MYC-like / : / Plant bHLH transcription factor, ACT-like domain / Transcription factor MYC/MYB N-terminal / bHLH-MYC and R2R3-MYB transcription factors N-terminal / Helix-loop-helix DNA-binding domain / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
Maltose/maltodextrin-binding periplasmic protein / Transcription factor MYC3 / Protein TIFY 10A / AFP homolog 2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Escherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / negative staining / Resolution: 10.4 Å
AuthorsZhou, X.E. / Zhang, Y. / Zhou, Y. / He, Q. / Cao, X. / Kariapper, L. / Suino-Powell, K. / Zhu, Y. / Zhang, F. / Karsten, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1922846 United States
CitationJournal: Plant Commun / Year: 2023
Title: Assembly of JAZ-JAZ and JAZ-NINJA complexes in jasmonate signaling.
Authors: X Edward Zhou / Yaguang Zhang / Jian Yao / Jie Zheng / Yuxin Zhou / Qing He / Javier Moreno / Vinh Q Lam / Xiaoman Cao / Koichi Sugimoto / Leidy Vanegas-Cano / Leena Kariapper / Kelly Suino- ...Authors: X Edward Zhou / Yaguang Zhang / Jian Yao / Jie Zheng / Yuxin Zhou / Qing He / Javier Moreno / Vinh Q Lam / Xiaoman Cao / Koichi Sugimoto / Leidy Vanegas-Cano / Leena Kariapper / Kelly Suino-Powell / Yuanye Zhu / Scott Novick / Patrick R Griffin / Feng Zhang / Gregg A Howe / Karsten Melcher /
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. ...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.
History
DepositionJun 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2023Provider: repository / Type: Initial release
Revision 1.0Jun 28, 2023Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 28, 2023Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 28, 2023Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 28, 2023Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 28, 2023Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Jun 28, 2023Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 28, 2023Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 28, 2023Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 28, 2023Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation / Item: _citation.journal_volume
Revision 1.2May 21, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1May 21, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcription factor MYC3
M: Maltose/maltodextrin-binding periplasmic protein
J: Protein TIFY 10A
N: AFP homolog 2


Theoretical massNumber of molelcules
Total (without water)138,3834
Polymers138,3834
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Transcription factor MYC3 / Basic helix-loop-helix protein 5 / AtbHLH5 / bHLH 5 / Protein ALTERED TRYPTOPHAN REGULATION 2 / ...Basic helix-loop-helix protein 5 / AtbHLH5 / bHLH 5 / Protein ALTERED TRYPTOPHAN REGULATION 2 / Transcription factor ATR2 / Transcription factor EN 36 / bHLH transcription factor bHLH005


Mass: 20972.973 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: MYC3, ATR2, BHLH5, EN36, At5g46760, MZA15.18 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9FIP9
#2: Protein Maltose/maltodextrin-binding periplasmic protein / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP


Mass: 44779.238 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: malE, Z5632, ECs5017 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P0AEY0
#3: Protein Protein TIFY 10A / Jasmonate ZIM domain-containing protein 1


Mass: 27640.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: TIFY10A, JAZ1, At1g19180, T29M8.5 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9LMA8
#4: Protein AFP homolog 2 / Novel interactor of JAZ


Mass: 44990.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AFPH2, NINJA, At4g28910, F25O24.30 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9SV55
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: MBP fused MYC JAZ NINJA complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: YES / Vitrification applied: NO
EM stainingType: NEGATIVE / Material: Uranyl Formate

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI SPIRIT
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 120 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 4500 nm / Nominal defocus min: 1400 nm
Image recordingElectron dose: 6 e/Å2 / Film or detector model: GATAN ORIUS SC600 (2.7k x 2.7k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 10.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 26340 / Symmetry type: POINT

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