6BYY

MEF2 CHIMERA/DNA Complex

  • Classification: TRANSCRIPTION/DNA
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2017-12-21 Released: 2018-01-31 
  • Deposition Author(s): Lei, X., Chen, L.
  • Funding Organization(s): National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.216 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The Cancer Mutation D83V Induces an alpha-Helix to beta-Strand Conformation Switch in MEF2B.

Lei, X.Kou, Y.Fu, Y.Rajashekar, N.Shi, H.Wu, F.Xu, J.Luo, Y.Chen, L.

(2018) J Mol Biol 430: 1157-1172

  • DOI: 10.1016/j.jmb.2018.02.012
  • Primary Citation of Related Structures:  
    6BYY, 6BZ1

  • PubMed Abstract: 
  • MEF2B is a major target of somatic mutations in non-Hodgkin lymphoma. Most of these mutations are non-synonymous substitutions of surface residues in the MADS-box/MEF2 domain. Among them, D83V is the most frequent mutation found in tumor cells. The link between this hotspot mutation and cancer is not well understood ...

    MEF2B is a major target of somatic mutations in non-Hodgkin lymphoma. Most of these mutations are non-synonymous substitutions of surface residues in the MADS-box/MEF2 domain. Among them, D83V is the most frequent mutation found in tumor cells. The link between this hotspot mutation and cancer is not well understood. Here we show that the D83V mutation induces a dramatic α-helix to β-strand switch in the MEF2 domain. Located in an α-helix region rich in β-branched residues, the D83V mutation not only removes the extensive helix stabilization interactions but also introduces an additional β-branched residue that further shifts the conformation equilibrium from α-helix to β-strand. Cross-database analyses of cancer mutations and chameleon sequences revealed a number of well-known cancer targets harboring β-strand favoring mutations in chameleon α-helices, suggesting a commonality of such conformational switch in certain cancers and a new factor to consider when stratifying the rapidly expanding cancer mutation data.


    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 ABCD95Homo sapiensMutation(s): 0 
Gene Names: MEF2AMEF2MEF2BXMEF2
Find proteins for Q02080 (Homo sapiens)
Explore Q02080 
Go to UniProtKB:  Q02080
NIH Common Fund Data Resources
PHAROS:  Q02080
Find proteins for Q02078 (Homo sapiens)
Explore Q02078 
Go to UniProtKB:  Q02078
NIH Common Fund Data Resources
PHAROS:  Q02078
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(P*AP*AP*CP*TP*AP*TP*TP*TP*AP*TP*AP*AP*GP*A)-3')E, K14Homo sapiens
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(P*TP*TP*CP*TP*TP*AP*TP*AP*AP*AP*TP*AP*GP*TP*T)-3')F, L15Homo sapiens
      Small Molecules
      Ligands 2 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      1PG
      Query on 1PG

      Download Ideal Coordinates CCD File 
      A
      2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
      C11 H24 O6
      SLNYBUIEAMRFSZ-UHFFFAOYSA-N
       Ligand Interaction
      TCE
      Query on TCE

      Download Ideal Coordinates CCD File 
      F
      3,3',3''-phosphanetriyltripropanoic acid
      C9 H15 O6 P
      PZBFGYYEXUXCOF-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.30 Å
      • R-Value Free: 0.266 
      • R-Value Work: 0.213 
      • R-Value Observed: 0.216 
      • Space Group: P 21 21 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 77.35α = 90
      b = 77.76β = 90
      c = 106.31γ = 90
      Software Package:
      Software NamePurpose
      PHENIXrefinement
      PDB_EXTRACTdata extraction

      Structure Validation

      View Full Validation Report



      Entry History & Funding Information

      Deposition Data

      • Deposited Date: 2017-12-21 
      • Released Date: 2018-01-31 
      • Deposition Author(s): Lei, X., Chen, L.

      Funding OrganizationLocationGrant Number
      National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United States--

      Revision History  (Full details and data files)

      • Version 1.0: 2018-01-31
        Type: Initial release
      • Version 1.1: 2018-03-07
        Changes: Database references
      • Version 1.2: 2018-04-11
        Changes: Data collection, Database references
      • Version 1.3: 2019-12-18
        Changes: Author supporting evidence