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 SCFCOI1 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 SCFCOI1, 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-CMIDJAZ10 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

    College of Plant Protection, Nanjing Agricultural University, 210095, Nanjing, Jiangsu Province, China.




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