[English] 日本語
Yorodumi
- PDB-8t2i: Negative stain EM assembly of MYC, JAZ, and NINJA complex -

+
Open data


ID or keywords:

Loading...

-
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 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
Ninja family / Tify domain binding domain / Tify domain binding domain / Tify domain / CO/COL/TOC1, conserved site / TIFY/JAZ family / Transcription factor AIB/MYC-like / tify domain / Jas motif / Tify domain profile. ...Ninja family / Tify domain binding domain / Tify domain binding domain / Tify domain / CO/COL/TOC1, conserved site / TIFY/JAZ family / Transcription factor AIB/MYC-like / tify domain / Jas motif / Tify domain profile. / TIFY / 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 DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / 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 1.1Nov 22, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation / Item: _citation.journal_volume

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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)

-
Processing

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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more