5T00

Human CTCF ZnF3-7 and methylated DNA complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history. 


Literature

Structural Basis for the Versatile and Methylation-Dependent Binding of CTCF to DNA.

Hashimoto, H., Wang, D., Horton, J.R., Zhang, X., Corces, V.G., Cheng, X.

(2017) Mol Cell 66: 711-720.e3

  • DOI: 10.1016/j.molcel.2017.05.004
  • Primary Citation of Related Structures:  
    5T00, 5T0U, 5UND, 5K5H, 5K5J, 5K5I, 5K5L, 5KKQ

  • PubMed Abstract: 

    • The multidomain CCCTC-binding factor (CTCF), containing a tandem array of 11 zinc fingers (ZFs), modulates the three-dimensional organization of chromatin. We crystallized the human CTCF DNA-binding domain in complex with a known CTCF-binding site. While ...

    The multidomain CCCTC-binding factor (CTCF), containing a tandem array of 11 zinc fingers (ZFs), modulates the three-dimensional organization of chromatin. We crystallized the human CTCF DNA-binding domain in complex with a known CTCF-binding site. While ZF2 does not make sequence-specific contacts, each finger of ZF3-7 contacts three bases of the 15-bp consensus sequence. Each conserved nucleotide makes base-specific hydrogen bonds with a particular residue. Most of the variable base pairs within the core sequence also engage in interactions with the protein. These interactions compensate for deviations from the consensus sequence, allowing CTCF to adapt to sequence variations. CTCF is sensitive to cytosine methylation at position 2, but insensitive at position 12 of the 15-bp core sequence. These differences can be rationalized structurally. Although included in crystallizations, ZF10 and ZF11 are not visible, while ZF8 and ZF9 span the backbone of the DNA duplex, conferring no sequence specificity but adding to overall binding stability.

    Organizational Affiliation: 

    Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road NE, Atlanta, GA 30322, USA; Department of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. Electronic address: xcheng5@mdanderson.org.



Macromolecules

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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Transcriptional repressor CTCF A, D150Homo sapiensMutation(s): 0 
Gene Names: CTCF
Find proteins for P49711 (Homo sapiens)
Explore P49711 
Go to UniProtKB:  P49711
NIH Common Fund Data Resources
PHAROS:  P49711
GTEx:  ENSG00000102974
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-TAG(5CM)GCCCCCTGCTGGC-3')B, E17synthetic construct
    • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-GCCAGCAGGGGG(5CM)GCTA-3')C, F17synthetic construct
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.19 Å
      • R-Value Free: 0.243 
      • R-Value Work: 0.218 
      • R-Value Observed: 0.220 
      • Space Group: P 1
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 40.99α = 98.33
      b = 44.91β = 92.4
      c = 86.8γ = 94.8
      Software Package:
      Software NamePurpose
      PHENIXrefinement
      XDSdata reduction
      XSCALEdata scaling
      PHASERphasing

      Structure Validation

      View Full Validation Report


      View more in-depth experimental data

      Entry History & Funding Information

      Deposition Data

      Funding OrganizationLocationGrant Number
      National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM049245

      Revision History 

      • Version 1.0: 2017-05-24
        Type: Initial release
      • Version 1.1: 2017-05-31
        Changes: Database references
      • Version 1.2: 2017-06-14
        Changes: Database references
      • Version 1.3: 2017-09-27
        Changes: Author supporting evidence
      • Version 1.4: 2019-12-25
        Changes: Author supporting evidence