5GNJ

Structure of a transcription factor and DNA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal Structure of Tetrameric Arabidopsis MYC2 Reveals the Mechanism of Enhanced Interaction with DNA.

Lian, T.F.Xu, Y.P.Li, L.F.Su, X.D.

(2017) Cell Rep 19: 1334-1342

  • DOI: 10.1016/j.celrep.2017.04.057

  • PubMed Abstract: 
  • Jasmonates (JAs) are essential plant hormones that play important roles in the regulation of plant growth and the response to environmental stress. In the JA signaling pathway, the core transcription factors are a class of basic helix-loop-helix (bHL ...

    Jasmonates (JAs) are essential plant hormones that play important roles in the regulation of plant growth and the response to environmental stress. In the JA signaling pathway, the core transcription factors are a class of basic helix-loop-helix (bHLH) proteins, including MYC2, MYC3, and MYC4, that have different regulatory capacities. Here, we report the 2.7 Å crystal structure of the MYC2 bHLH domain complexed with G-box DNA, showing a cis-tetrameric structure. Biochemical assays confirmed that full-length MYC2 forms a stable homo-tetramer both in solution and in DNA-bound states, whereas MYC3 forms only a homodimer. Isothermal titration calorimetry (ITC) assays demonstrated that tetramerization enhanced DNA binding affinity, and fluorescence resonance energy transfer (FRET) assay indicated DNA looping potential of tetrameric MYC2. Luciferase assay further confirmed the importance of tetramerization in transcriptional regulation. Our studies provide a mechanistic explanation for the regulatory differences of MYC transcription factors.


    Organizational Affiliation

    State Key Laboratory of Protein and Plant Gene Research and Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transcription factor MYC2
G, I, A, B, E, F, M, N
89Arabidopsis thalianaMutation(s): 0 
Gene Names: MYC2 (BHLH6, EN38, JAI1, JIN1, RAP1, RD22BP1, ZBF1)
Find proteins for Q39204 (Arabidopsis thaliana)
Go to UniProtKB:  Q39204
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*GP*GP*AP*AP*CP*AP*CP*GP*TP*GP*AP*CP*CP*C)-3')K,C,H,O15synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*GP*GP*GP*TP*CP*AP*CP*GP*TP*GP*TP*TP*CP*C)-3')L,D,J,P15synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.206 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 77.100α = 90.00
b = 79.700β = 105.00
c = 102.800γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-07-21 
  • Released Date: 2017-05-10 
  • Deposition Author(s): Lian, T., Xu, Y., Su, X.

Funding OrganizationLocationGrant Number
China--

Revision History 

  • Version 1.0: 2017-05-10
    Type: Initial release
  • Version 1.1: 2017-12-06
    Type: Database references