8t2i

From Proteopedia

(Difference between revisions)

Current revision

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

Structural highlights

8t2i is a 4 chain structure with sequence from Arabidopsis thaliana and Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Electron Microscopy, Resolution 10.4Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

MYC3_ARATH Transcription factor involved in tryptophan, jasmonic acid (JA) and other stress-responsive gene regulation. With MYC2 and MYC4, controls additively subsets of JA-dependent responses. Can form complexes with all known glucosinolate-related MYBs to regulate glucosinolate biosynthesis. Binds to the G-box (5'-CACGTG-3') of promoters. Activates multiple TIFY/JAZ promoters.^[1] ^[2] ^[3] ^[4] ^[5]

Publication Abstract from PubMed

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. In the absence of JA, JAZ proteins bind and inhibit MYC through the assembly of MYC-JAZ-NINJA-TPL repressor complexes. However, JAZ and NINJA are predicted to be largely intrinsically unstructured, which 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. In 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 ZIM motif mediates JAZ-JAZ and JAZ-NINJA interactions through separate surfaces, and further suggest that NINJA modulates JAZ dimerization. This study advances knowledge of JA signaling by providing insight into dynamics, interactions, and structure of the JAZ-NINJA core of the JA repressor complex.

Assembly of JAZ-JAZ and JAZ-NINJA complexes in jasmonate signaling.,Zhou XE, Zhang Y, Yao J, Zheng J, Zhou Y, He Q, Moreno J, Lam VQ, Cao X, Sugimoto K, Vanegas-Cano L, Kariapper L, Suino-Powell K, Zhu Y, Novick S, Griffin PR, Zhang F, Howe GA, Melcher K Plant Commun. 2023 Jun 14:100639. doi: 10.1016/j.xplc.2023.100639. PMID:37322867^[6]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Smolen GA, Pawlowski L, Wilensky SE, Bender J. Dominant alleles of the basic helix-loop-helix transcription factor ATR2 activate stress-responsive genes in Arabidopsis. Genetics. 2002 Jul;161(3):1235-46. PMID:12136026
↑ Cheng Z, Sun L, Qi T, Zhang B, Peng W, Liu Y, Xie D. The bHLH transcription factor MYC3 interacts with the Jasmonate ZIM-domain proteins to mediate jasmonate response in Arabidopsis. Mol Plant. 2011 Mar;4(2):279-88. doi: 10.1093/mp/ssq073. Epub 2011 Jan 17. PMID:21242320 doi:http://dx.doi.org/10.1093/mp/ssq073
↑ Niu Y, Figueroa P, Browse J. Characterization of JAZ-interacting bHLH transcription factors that regulate jasmonate responses in Arabidopsis. J Exp Bot. 2011 Mar;62(6):2143-54. doi: 10.1093/jxb/erq408. Epub 2011 Feb 14. PMID:21321051 doi:http://dx.doi.org/10.1093/jxb/erq408
↑ Fernandez-Calvo P, Chini A, Fernandez-Barbero G, Chico JM, Gimenez-Ibanez S, Geerinck J, Eeckhout D, Schweizer F, Godoy M, Franco-Zorrilla JM, Pauwels L, Witters E, Puga MI, Paz-Ares J, Goossens A, Reymond P, De Jaeger G, Solano R. The Arabidopsis bHLH transcription factors MYC3 and MYC4 are targets of JAZ repressors and act additively with MYC2 in the activation of jasmonate responses. Plant Cell. 2011 Feb;23(2):701-15. doi: 10.1105/tpc.110.080788. Epub 2011 Feb 18. PMID:21335373 doi:http://dx.doi.org/10.1105/tpc.110.080788
↑ Schweizer F, Fernandez-Calvo P, Zander M, Diez-Diaz M, Fonseca S, Glauser G, Lewsey MG, Ecker JR, Solano R, Reymond P. Arabidopsis basic helix-loop-helix transcription factors MYC2, MYC3, and MYC4 regulate glucosinolate biosynthesis, insect performance, and feeding behavior. Plant Cell. 2013 Aug;25(8):3117-32. doi: 10.1105/tpc.113.115139. Epub 2013 Aug, 13. PMID:23943862 doi:http://dx.doi.org/10.1105/tpc.113.115139
↑ Zhou XE, Zhang Y, Yao J, Zheng J, Zhou Y, He Q, Moreno J, Lam VQ, Cao X, Sugimoto K, Vanegas-Cano L, Kariapper L, Suino-Powell K, Zhu Y, Novick S, Griffin PR, Zhang F, Howe GA, Melcher K. Assembly of JAZ-JAZ and JAZ-NINJA complexes in jasmonate signaling. Plant Commun. 2023 Jun 14:100639. PMID:37322867 doi:10.1016/j.xplc.2023.100639

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/8t2i"

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 8t2i is ON HOLD  until Paper Publication
+==Negative stain EM assembly of MYC, JAZ, and NINJA complex==
+<StructureSection load='8t2i' size='340' side='right'caption='[[8t2i]], [[Resolution|resolution]] 10.40&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[8t2i]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana] and [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8T2I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8T2I FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 10.4&#8491;</td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=8t2i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8t2i OCA], [https://pdbe.org/8t2i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8t2i RCSB], [https://www.ebi.ac.uk/pdbsum/8t2i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8t2i ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/MYC3_ARATH MYC3_ARATH] Transcription factor involved in tryptophan, jasmonic acid (JA) and other stress-responsive gene regulation. With MYC2 and MYC4, controls additively subsets of JA-dependent responses. Can form complexes with all known glucosinolate-related MYBs to regulate glucosinolate biosynthesis. Binds to the G-box (5'-CACGTG-3') of promoters. Activates multiple TIFY/JAZ promoters.<ref>PMID:12136026</ref> <ref>PMID:21242320</ref> <ref>PMID:21321051</ref> <ref>PMID:21335373</ref> <ref>PMID:23943862</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+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. In the absence of JA, JAZ proteins bind and inhibit MYC through the assembly of MYC-JAZ-NINJA-TPL repressor complexes. However, JAZ and NINJA are predicted to be largely intrinsically unstructured, which 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. In 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 ZIM motif mediates JAZ-JAZ and JAZ-NINJA interactions through separate surfaces, and further suggest that NINJA modulates JAZ dimerization. This study advances knowledge of JA signaling by providing insight into dynamics, interactions, and structure of the JAZ-NINJA core of the JA repressor complex.
-Authors: Zhou, X.E., Zhang, Y., Zhou, Y., He, Q., Cao, X., Kariapper, L., Suino-Powell, K., Zhu, Y., Zhang, F., Karsten, M.
+Assembly of JAZ-JAZ and JAZ-NINJA complexes in jasmonate signaling.,Zhou XE, Zhang Y, Yao J, Zheng J, Zhou Y, He Q, Moreno J, Lam VQ, Cao X, Sugimoto K, Vanegas-Cano L, Kariapper L, Suino-Powell K, Zhu Y, Novick S, Griffin PR, Zhang F, Howe GA, Melcher K Plant Commun. 2023 Jun 14:100639. doi: 10.1016/j.xplc.2023.100639. PMID:37322867<ref>PMID:37322867</ref>
-Description: Negative stain EM assembly of MYC, JAZ, and NINJA complex
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Zhou, X.E]]
+<div class="pdbe-citations 8t2i" style="background-color:#fffaf0;"></div>
-[[Category: Karsten, M]]
+== References ==
-[[Category: Zhang, Y]]
+<references/>
-[[Category: Cao, X]]
+__TOC__
-[[Category: He, Q]]
+</StructureSection>
-[[Category: Kariapper, L]]
+[[Category: Arabidopsis thaliana]]
-[[Category: Zhu, Y]]
+[[Category: Escherichia coli]]
-[[Category: Zhang, F]]
+[[Category: Large Structures]]
-[[Category: Suino-Powell, K]]
+[[Category: Cao X]]
-[[Category: Zhou, Y]]
+[[Category: He Q]]
+[[Category: Kariapper L]]
+[[Category: Karsten M]]
+[[Category: Suino-Powell K]]
+[[Category: Zhang F]]
+[[Category: Zhang Y]]
+[[Category: Zhou XE]]
+[[Category: Zhou Y]]
+[[Category: Zhu Y]]

8t2i

From Proteopedia

Current revision

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

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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