6WC2

Crystal Structure of a Ternary MEF2 Chimera/NKX2-5/myocardin enhancer DNA Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal Structures of Ternary Complexes of MEF2 and NKX2-5 Bound to DNA Reveal a Disease Related Protein-Protein Interaction Interface.

Lei, X.Zhao, J.Sagendorf, J.M.Rajashekar, N.Xu, J.Dantas Machado, A.C.Sen, C.Rohs, R.Feng, P.Chen, L.

(2020) J Mol Biol 432: 5499-5508

  • DOI: 10.1016/j.jmb.2020.07.004
  • Primary Citation of Related Structures:  
    6WC2, 6WC5

  • PubMed Abstract: 
  • MEF2 and NKX2-5 transcription factors interact with each other in cardiogenesis and are necessary for normal heart formation. Despite evidence suggesting that these two transcription factors function synergistically and possibly through direct physical interactions, molecular mechanisms by which they interact are not clear ...

    MEF2 and NKX2-5 transcription factors interact with each other in cardiogenesis and are necessary for normal heart formation. Despite evidence suggesting that these two transcription factors function synergistically and possibly through direct physical interactions, molecular mechanisms by which they interact are not clear. Here we determined the crystal structures of ternary complexes of MEF2 and NKX2-5 bound to myocardin enhancer DNA in two crystal forms. These crystal structures are the first example of human MADS-box/homeobox ternary complex structures involved in cardiogenesis. Our structures reveal two possible modes of interactions between MEF2 and NKX2-5: MEF2 and NKX bind to adjacent DNA sites to recognize DNA in cis; and MEF2 and NKX bind to different DNA strands to interact with each other in trans via a conserved protein-protein interface observed in both crystal forms. Disease-related mutations are mapped to the observed protein-protein interface. Our structural studies provide a starting point to understand and further study the molecular mechanisms of the interactions between MEF2 and NKX2.5 and their roles in cardiogenesis.


    Organizational Affiliation

    Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA; Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA; USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA. Electronic address: linchen@usc.edu.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MEF2 Chimera,Myocyte-specific enhancer factor 2B,Myocyte-specific enhancer factor 2AA, B, C, D, I, J95Homo sapiensMutation(s): 0 
Gene Names: MEF2AMEF2MEF2BXMEF2
UniProt & NIH Common Fund Data Resources
Find proteins for Q02080 (Homo sapiens)
Explore Q02080 
Go to UniProtKB:  Q02080
PHAROS:  Q02080
Find proteins for Q02078 (Homo sapiens)
Explore Q02078 
Go to UniProtKB:  Q02078
PHAROS:  Q02078
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Homeobox protein Nkx-2.5M, N, O61Homo sapiensMutation(s): 0 
Gene Names: NKX2-5CSXNKX2.5NKX2E
UniProt & NIH Common Fund Data Resources
Find proteins for P52952 (Homo sapiens)
Explore P52952 
Go to UniProtKB:  P52952
PHAROS:  P52952
Protein Feature View
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
Myocardin Enhancer DNAE, G, K21synthetic construct
Protein Feature View
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsLengthOrganismImage
Myocardin Enhancer DNAF, H, L21synthetic construct
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.37α = 90
b = 133.9β = 90
c = 140.04γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2020-03-29 
  • Released Date: 2020-07-22 
  • Deposition Author(s): Lei, X., Chen, L.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States5U54DK107981

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-22
    Type: Initial release
  • Version 1.1: 2020-07-29
    Changes: Database references
  • Version 1.2: 2020-09-30
    Changes: Database references