4X9J

EGR-1 with Doubly Methylated DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural impact of complete CpG methylation within target DNA on specific complex formation of the inducible transcription factor Egr-1.

Zandarashvili, L.White, M.A.Esadze, A.Iwahara, J.

(2015) FEBS Lett 589: 1748-1753

  • DOI: 10.1016/j.febslet.2015.05.022
  • Primary Citation of Related Structures:  
    4X9J

  • PubMed Abstract: 
  • The inducible transcription factor Egr-1 binds specifically to 9-bp target sequences containing two CpG sites that can potentially be methylated at four cytosine bases. Although it appears that complete CpG methylation would make an unfavorable steric clash in the previous crystal structures of the complexes with unmethylated or partially methylated DNA, our affinity data suggest that DNA recognition by Egr-1 is insensitive to CpG methylation ...

    The inducible transcription factor Egr-1 binds specifically to 9-bp target sequences containing two CpG sites that can potentially be methylated at four cytosine bases. Although it appears that complete CpG methylation would make an unfavorable steric clash in the previous crystal structures of the complexes with unmethylated or partially methylated DNA, our affinity data suggest that DNA recognition by Egr-1 is insensitive to CpG methylation. We have determined, at a 1.4-Å resolution, the crystal structure of the Egr-1 zinc-finger complex with completely methylated target DNA. Structural comparison of the three different methylation states reveals why Egr-1 can recognize the target sequences regardless of CpG methylation.


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      (2014) Genes Dev 28: 2304

    Organizational Affiliation

    Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555-1068, USA. Electronic address: j.iwahara@utmb.edu.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Early growth response protein 1A89Homo sapiensMutation(s): 0 
Gene Names: EGR1KROX24ZNF225
Find proteins for P18146 (Homo sapiens)
Explore P18146 
Go to UniProtKB:  P18146
NIH Common Fund Data Resources
PHAROS:  P18146
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*AP*GP*(5CM)P*GP*TP*GP*GP*GP*(5CM)P*GP*T)-3')B11synthetic construct
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*TP*AP*(5CM)P*GP*CP*CP*CP*AP*(5CM)P*GP*C)-3')C11synthetic construct
      Small Molecules
      Ligands 1 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      ZN
      Query on ZN

      Download Ideal Coordinates CCD File 
      D [auth A], E [auth A], F [auth A]ZINC ION
      Zn
      PTFCDOFLOPIGGS-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 1.41 Å
      • R-Value Free: 0.200 
      • R-Value Work: 0.172 
      • R-Value Observed: 0.174 
      • Space Group: C 2 2 21
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 44.009α = 90
      b = 55.989β = 90
      c = 128.952γ = 90
      Software Package:
      Software NamePurpose
      PHENIXrefinement
      HKL-2000data reduction
      PDB_EXTRACTdata extraction
      HKL-2000data scaling
      PHENIXphasing

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2015-05-13
        Type: Initial release
      • Version 1.1: 2015-06-03
        Changes: Database references
      • Version 1.2: 2015-07-15
        Changes: Database references
      • Version 1.3: 2017-09-27
        Changes: Author supporting evidence, Database references, Derived calculations, Source and taxonomy