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PDBsum entry 5k5h
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Transcription/DNA
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PDB id
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5k5h
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References listed in PDB file
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Key reference
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Title
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Structural basis for the versatile and methylation-Dependent binding of ctcf to DNA.
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Authors
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H.Hashimoto,
D.Wang,
J.R.Horton,
X.Zhang,
V.G.Corces,
X.Cheng.
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Ref.
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Mol Cell, 2017,
66,
711.
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PubMed id
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Abstract
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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.
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