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 1.4 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: https://doi.org/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.

    Related Citations: 
    • Wilms tumor protein recognizes 5-carboxylcytosine within a specific DNA sequence.
      Hashimoto, H., Olanrewaju, Y.O., Zheng, Y., Wilson, G.G., Zhang, X., Cheng, X.
      (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)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Early growth response protein 189Homo sapiensMutation(s): 0 
Gene Names: EGR1, KROX24, ZNF225
UniProt & NIH Common Fund Data Resources
Find proteins for P18146 (Homo sapiens)
Explore P18146 
Go to UniProtKB:  P18146
PHAROS:  P18146
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18146
Protein Feature View
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(*AP*GP*(5CM)P*GP*TP*GP*GP*GP*(5CM)P*GP*T)-3')11synthetic construct
Protein Feature View
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA (5'-D(*TP*AP*(5CM)P*GP*CP*CP*CP*AP*(5CM)P*GP*C)-3')11synthetic construct
Protein Feature View
Expand
  • Reference Sequence
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



View more in-depth experimental data
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
  • Version 1.4: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description