3KOV

Structure of MEF2A bound to DNA reveals a completely folded MADS-box/MEF2 domain that recognizes DNA and recruits transcription co-factors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of the MADS-box/MEF2 Domain of MEF2A Bound to DNA and Its Implication for Myocardin Recruitment.

Wu, Y.Dey, R.Han, A.Jayathilaka, N.Philips, M.Ye, J.Chen, L.

(2010) J.Mol.Biol. 397: 520-533

  • DOI: 10.1016/j.jmb.2010.01.067

  • PubMed Abstract: 
  • Myocyte enhancer factor 2 (MEF2) regulates specific gene expression in diverse developmental programs and adaptive responses. MEF2 recognizes DNA and interacts with transcription cofactors through a highly conserved N-terminal domain referred to as t ...

    Myocyte enhancer factor 2 (MEF2) regulates specific gene expression in diverse developmental programs and adaptive responses. MEF2 recognizes DNA and interacts with transcription cofactors through a highly conserved N-terminal domain referred to as the MADS-box/MEF2 domain. Here we present the crystal structure of the MADS-box/MEF2 domain of MEF2A bound to DNA. In contrast to previous structural studies showing that the MEF2 domain of MEF2A is partially unstructured, the present study reveals that the MEF2 domain participates with the MADS-box in both dimerization and DNA binding as a single domain. The sequence divergence at and immediately following the C-terminal end of the MEF2 domain may allow different MEF2 dimers to recognize different DNA sequences in the flanking regions. The current structure also suggests that the ligand-binding pocket previously observed in the Cabin1-MEF2B-DNA complex and the HDAC9 (histone deacetylase 9)-MEF2B-DNA complex is not induced by cofactor binding but rather preformed by intrinsic folding. However, the structure of the ligand-binding pocket does undergo subtle but significant conformational changes upon cofactor binding. On the basis of these observations, we generated a homology model of MEF2 bound to a myocardin family protein, MASTR, that acts as a potent coactivator of MEF2-dependent gene expression. The model shows excellent shape and chemical complementarity at the binding interface and is consistent with existing mutagenesis data. The apo structure presented here can also serve as a target for virtual screening and soaking studies of small molecules that can modulate the function of MEF2 as research tools and therapeutic leads.


    Organizational Affiliation

    Division of Molecular and Computational Biology, Departments of Biological Sciences and Chemistry, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, RRI 204c, 1050 Childs Way, Los Angeles, CA 90089, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Myocyte-specific enhancer factor 2A
A, B, I, J
90Homo sapiensMutation(s): 0 
Gene Names: MEF2A (MEF2)
Find proteins for Q02078 (Homo sapiens)
Go to Gene View: MEF2A
Go to UniProtKB:  Q02078
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*AP*CP*TP*AP*TP*TP*TP*AP*TP*AP*AP*G)-3')C,K13N/A
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*CP*TP*TP*AP*TP*AP*AP*AP*TP*AP*GP*T)-3')D,L13N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.221 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 77.801α = 90.00
b = 77.960β = 90.00
c = 106.794γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-02-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description
  • Version 1.3: 2018-04-04
    Type: Data collection