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Open data
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Basic information
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Title | Negative stain EM assembly of MYC, JAZ, and NINJA complex | |||||||||
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![]() | Jasmonate signaling / MYC / JAZ / NINJA / SIGNALING PROTEIN | |||||||||
Function / homology | ![]() regulation of cellular response to alkaline pH / regulation of defense response / regulation of leaf morphogenesis / extracellular ATP signaling / regulation of jasmonic acid mediated signaling pathway / anthocyanin-containing compound biosynthetic process / stomatal complex development / jasmonic acid mediated signaling pathway / pollen development / flower development ...regulation of cellular response to alkaline pH / regulation of defense response / regulation of leaf morphogenesis / extracellular ATP signaling / regulation of jasmonic acid mediated signaling pathway / anthocyanin-containing compound biosynthetic process / stomatal complex development / jasmonic acid mediated signaling pathway / pollen development / flower development / response to jasmonic acid / bHLH transcription factor binding / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / defense response / response to wounding / outer membrane-bounded periplasmic space / protein dimerization activity / transcription cis-regulatory region binding / 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 / identical protein binding / nucleus / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 10.4 Å | |||||||||
![]() | Zhou XE / Zhang Y / Zhou Y / He Q / Cao X / Kariapper L / Suino-Powell K / Zhu Y / Zhang F / Karsten M | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 34.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 18.1 KB 18.1 KB | Display Display | ![]() |
Images | ![]() | 32.7 KB | ||
Filedesc metadata | ![]() | 6.2 KB | ||
Others | ![]() ![]() | 37.4 MB 37.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 570.2 KB | Display | ![]() |
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Full document | ![]() | 569.8 KB | Display | |
Data in XML | ![]() | 11.9 KB | Display | |
Data in CIF | ![]() | 13.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8t2iMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 2.3 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_40983_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_40983_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : MBP fused MYC JAZ NINJA complex
Entire | Name: MBP fused MYC JAZ NINJA complex |
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Components |
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-Supramolecule #1: MBP fused MYC JAZ NINJA complex
Supramolecule | Name: MBP fused MYC JAZ NINJA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Transcription factor MYC3
Macromolecule | Name: Transcription factor MYC3 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 20.972973 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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 |
-Macromolecule #2: Maltose/maltodextrin-binding periplasmic protein
Macromolecule | Name: Maltose/maltodextrin-binding periplasmic protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 44.779238 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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 |
-Macromolecule #3: Protein TIFY 10A
Macromolecule | Name: Protein TIFY 10A / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 27.640266 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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 |
-Macromolecule #4: AFP homolog 2
Macromolecule | Name: AFP homolog 2 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 44.990797 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | negative staining |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.8 |
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Staining | Type: NEGATIVE / Material: Uranyl Formate |
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Electron microscopy
Microscope | FEI TECNAI SPIRIT |
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Image recording | Film or detector model: GATAN ORIUS SC600 (2.7k x 2.7k) / Average electron dose: 6.0 e/Å2 |
Electron beam | Acceleration voltage: 120 kV / Electron source: ![]() |
Electron optics | Illumination 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 model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 10.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 26340 |
Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: NOT APPLICABLE |