5T0Q

Crystal structure of the Myc3 N-terminal domain [44-242] in complex with JAZ10 Jas domain [166-192] from arabidopsis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

Structural insights into alternative splicing-mediated desensitization of jasmonate signaling.

Zhang, F.Ke, J.Zhang, L.Chen, R.Sugimoto, K.Howe, G.A.Xu, H.E.Zhou, M.He, S.Y.Melcher, K.

(2017) Proc. Natl. Acad. Sci. U.S.A. 114: 1720-1725

  • DOI: 10.1073/pnas.1616938114
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Jasmonate ZIM-domain (JAZ) transcriptional repressors play a key role in regulating jasmonate (JA) signaling in plants. Below a threshold concentration of jasmonoyl isoleucine (JA-Ile), the active form of JA, the C-terminal Jas motif of JAZ proteins ...

    Jasmonate ZIM-domain (JAZ) transcriptional repressors play a key role in regulating jasmonate (JA) signaling in plants. Below a threshold concentration of jasmonoyl isoleucine (JA-Ile), the active form of JA, the C-terminal Jas motif of JAZ proteins binds MYC transcription factors to repress JA signaling. With increasing JA-Ile concentration, the Jas motif binds to JA-Ile and the COI1 subunit of the SCF COI1 E3 ligase, which mediates ubiquitination and proteasomal degradation of JAZ repressors, resulting in derepression of MYC transcription factors. JA signaling subsequently becomes desensitized, in part by feedback induction of JAZ splice variants that lack the C-terminal Jas motif but include an N-terminal cryptic MYC-interaction domain (CMID). The CMID sequence is dissimilar to the Jas motif and is incapable of recruiting SCF COI1 , allowing CMID-containing JAZ splice variants to accumulate in the presence of JA and to re-repress MYC transcription factors as an integral part of reestablishing signal homeostasis. The mechanism by which the CMID represses MYC transcription factors remains elusive. Here we describe the crystal structure of the MYC3-CMID JAZ10 complex. In contrast to the Jas motif, which forms a single continuous helix when bound to MYC3, the CMID adopts a loop-helix-loop-helix architecture with modular interactions with both the Jas-binding groove and the backside of the Jas-interaction domain of MYC3. This clamp-like interaction allows the CMID to bind MYC3 tightly and block access of MED25 (a subunit of the Mediator coactivator complex) to the MYC3 transcriptional activation domain, shedding light on the enigmatic mechanism by which JAZ splice variants desensitize JA signaling.


    Organizational Affiliation

    Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI 48824; mgzhou@njau.edu.cn hes@msu.edu karsten.melcher@vai.org.,Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824.,Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI 48824.,Howard Hughes Medical Institute, Michigan State University, East Lansing, MI 48824.,Department of Plant Biology, Michigan State University, East Lansing, MI 48824.,College of Plant Protection, Nanjing Agricultural University, 210095, Nanjing, Jiangsu Province, China.,Laboratory of Structural Biology and Biochemistry, Van Andel Research Institute, Grand Rapids, MI 49503.,State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China.,Key Laboratory of Receptor Research, VARI-SIMM Center, Center for Structure and Function of Drug Targets, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,Laboratory of Structural Sciences, Van Andel Research Institute, Grand Rapids, MI 49503.,College of Plant Protection, Nanjing Agricultural University, 210095, Nanjing, Jiangsu Province, China; mgzhou@njau.edu.cn hes@msu.edu karsten.melcher@vai.org.,Laboratory of Structural Biology and Biochemistry, Van Andel Research Institute, Grand Rapids, MI 49503; mgzhou@njau.edu.cn hes@msu.edu karsten.melcher@vai.org.,Plant Resilience Institute, Michigan State University, East Lansing, MI 48824.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transcription factor MYC3
A
199Arabidopsis thalianaMutation(s): 0 
Gene Names: MYC3 (ATR2, BHLH5, EN36)
Find proteins for Q9FIP9 (Arabidopsis thaliana)
Go to UniProtKB:  Q9FIP9
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Protein TIFY 9
B
27Arabidopsis thalianaMutation(s): 0 
Gene Names: TIFY9 (JAS1, JAZ10)
Find proteins for Q93ZM9 (Arabidopsis thaliana)
Go to UniProtKB:  Q93ZM9
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.195 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 86.098α = 90.00
b = 86.098β = 90.00
c = 57.871γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney DiseaseUnited StatesDK071662
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM102545
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM104212

Revision History 

  • Version 1.0: 2017-01-25
    Type: Initial release
  • Version 1.1: 2017-02-15
    Type: Database references
  • Version 1.2: 2017-02-22
    Type: Database references
  • Version 1.3: 2017-09-20
    Type: Author supporting evidence
  • Version 1.4: 2017-11-01
    Type: Author supporting evidence
  • Version 1.5: 2017-11-29
    Type: Database references