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- EMDB-40983: Negative stain EM assembly of MYC, JAZ, and NINJA complex -

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Basic information

Entry
Database: EMDB / ID: EMD-40983
TitleNegative stain EM assembly of MYC, JAZ, and NINJA complex
Map data
Sample
  • Complex: MBP fused MYC JAZ NINJA complex
    • Protein or peptide: Transcription factor MYC3
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein
    • Protein or peptide: Protein TIFY 10A
    • Protein or peptide: AFP homolog 2
KeywordsJasmonate signaling / MYC / JAZ / NINJA / SIGNALING PROTEIN
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 / bHLH transcription factor binding / flower development / 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 / bHLH transcription factor binding / flower development / 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. / Bacterial extracellular solute-binding protein / 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
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)
Methodsingle particle reconstruction / negative staining / Resolution: 10.4 Å
AuthorsZhou XE / Zhang Y / Zhou Y / He Q / Cao X / Kariapper L / Suino-Powell K / Zhu Y / Zhang F / Karsten M
Funding support United States, 1 items
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, 2023-
Header (metadata) releaseJun 28, 2023-
Map releaseJun 28, 2023-
UpdateNov 22, 2023-
Current statusNov 22, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40983.png

Downloads & links

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Map

FileDownload / File: emd_40983.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.3 Å/pix.
x 250 pix.
= 575. Å		2.3 Å/pix.
x 250 pix.
= 575. Å		2.3 Å/pix.
x 250 pix.
= 575. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.3 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-0.7961597 - 6.1584063
Average (Standard dev.)-0.025577713 (±0.16901806)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions250250250
Spacing250250250
CellA=B=C: 575.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_40983_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_40983_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : MBP fused MYC JAZ NINJA complex

EntireName: MBP fused MYC JAZ NINJA complex
Components
  • Complex: MBP fused MYC JAZ NINJA complex
    • Protein or peptide: Transcription factor MYC3
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein
    • Protein or peptide: Protein TIFY 10A
    • Protein or peptide: AFP homolog 2

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Supramolecule #1: MBP fused MYC JAZ NINJA complex

SupramoleculeName: MBP fused MYC JAZ NINJA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: Transcription factor MYC3

MacromoleculeName: Transcription factor MYC3 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 20.972973 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
EDTLQQRLQA LIESAGENWT YAIFWQISHD FDSSTGDNTV ILGWGDGYYK GEEDKEKKKN NTNTAEQEHR KRVIRELNSL ISGGIGVSD ESNDEEVTDT EWFFLVSMTQ SFVNGVGLPG ESFLNSRVIW LSGSGALTGS GCERAGQGQI YGLKTMVCIA T QNGVVELG SSEVISQSSD LMHKVNNLFN FN

UniProtKB: Transcription factor MYC3

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Macromolecule #2: Maltose/maltodextrin-binding periplasmic protein

MacromoleculeName: Maltose/maltodextrin-binding periplasmic protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 44.779238 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MKHHHHHHHH HHSSDYKDDD DKGENLYFQG SKIEEGKLVI WINGDKGYNG LAEVGKKFEK DTGIKVTVEH PDKLEEKFPQ VAATGDGPD IIFWAHDRFG GYAQSGLLAE ITPDKAFQDK LYPFTWDAVR YNGKLIAYPI AVEALSLIYN KDLLPNPPKT W EEIPALDK ...String:
MKHHHHHHHH HHSSDYKDDD DKGENLYFQG SKIEEGKLVI WINGDKGYNG LAEVGKKFEK DTGIKVTVEH PDKLEEKFPQ VAATGDGPD IIFWAHDRFG GYAQSGLLAE ITPDKAFQDK LYPFTWDAVR YNGKLIAYPI AVEALSLIYN KDLLPNPPKT W EEIPALDK ELKAKGKSAL MFNLQEPYFT WPLIAADGGY AFKYENGKYD IKDVGVDNAG AKAGLTFLVD LIKNKHMNAD TD YSIAEAA FNKGETAMTI NGPWAWSNID TSKVNYGVTV LPTFKGQPSK PFVGVLSAGI NAASPNKELA KEFLENYLLT DEG LEAVNK DKPLGAVALK SYEEELAKDP RIAATMENAQ KGEIMPNIPQ MSAFWYAVRT AVINAASGRQ TVDEALKDAQ TNNA AAEF

UniProtKB: Maltose/maltodextrin-binding periplasmic protein

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Macromolecule #3: Protein TIFY 10A

MacromoleculeName: Protein TIFY 10A / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 27.640266 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSSSMECSEF VGSRRFTGKK PSFSQTCSRL SQYLKENGSF GDLSLGMACK PDVNGTLGNS RQPTTTMSLF PCEASNMDSM VQDVKPTNL FPRQPSFSSS SSSLPKEDVL KMTQTTRSVK PESQTAPLTI FYAGQVIVFN DFSAEKAKEV INLASKGTAN S LAKNQTDI ...String:
MSSSMECSEF VGSRRFTGKK PSFSQTCSRL SQYLKENGSF GDLSLGMACK PDVNGTLGNS RQPTTTMSLF PCEASNMDSM VQDVKPTNL FPRQPSFSSS SSSLPKEDVL KMTQTTRSVK PESQTAPLTI FYAGQVIVFN DFSAEKAKEV INLASKGTAN S LAKNQTDI RSNIATIANQ VPHPRKTTTQ EPIQSSPTPL TELPIARRAS LHRFLEKRKD RVTSKAPYQL CDPAKASSNP QT TGNMSWL GLAAEI

UniProtKB: Protein TIFY 10A

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Macromolecule #4: AFP homolog 2

MacromoleculeName: AFP homolog 2 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 44.990797 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MDDDNGLELS LGLSCGGSTG KAKGNNNNNA GSSSENYRAE GGDRSAKVID DFKNFLHPTS QRPAEPSSGS QRSDSGQQPP QNFFNDLSK APTTEAEAST KPLWVEDESR KEAGNKRKFG FPGMNDDKKK EKDSSHVDMH EKKTKASHVS TATDEGSTAE N EDVAESEV ...String:
MDDDNGLELS LGLSCGGSTG KAKGNNNNNA GSSSENYRAE GGDRSAKVID DFKNFLHPTS QRPAEPSSGS QRSDSGQQPP QNFFNDLSK APTTEAEAST KPLWVEDESR KEAGNKRKFG FPGMNDDKKK EKDSSHVDMH EKKTKASHVS TATDEGSTAE N EDVAESEV GGGSSSNHAK EVVRPPTDTN IVDNLTGQRR SNHGGSGTEE FTMRNMSYTV PFTVHPQNVV TSMPYSLPTK ES GQHAAAT SLLQPNANAG NLPIMFGYSP VQLPMLDKDG SGGIVALSQS PFAGRVPSNS ATAKGEGKQP VAEEGSSEDA SER PTGDNS NLNTAFSFDF SAIKPGMAAD VKFGGSGARP NLPWVSTTGS GPHGRTISGV TYRYNANQIK IVCACHGSHM SPEE FVRHA SEEYVSPESS MGMTAASAHT

UniProtKB: AFP homolog 2

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.8
StainingType: NEGATIVE / Material: Uranyl Formate

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Image recordingFilm or detector model: GATAN ORIUS SC600 (2.7k x 2.7k) / Average electron dose: 6.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.5 µm / Nominal defocus min: 1.4000000000000001 µm
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4rru

Final reconstructionResolution.type: BY AUTHOR / Resolution: 10.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 26340
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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