5mC interactions in PDB entry 5T00 auto-curated with SNAP

Last updated on 2019-09-30 by Xiang-Jun Lu <xiangjun@x3dna.org>. The block schematics were created with DSSR and rendered using PyMOL.

Summary information and primary citation [schematics · contacts · top · homepage · tutorial]

transcription regulator-DNA
X-ray (2.19 Å)
Human ctcf znf3-7 and methylated DNA complex
List of 4 5mC-amino acid contacts:
  1. B.5CM4: other-contacts is-WC-paired is-in-duplex [+]:GcG/cGC
  2. C.5CM13: stacking-with-A.ARG339 is-WC-paired is-in-duplex [-]:cGC/GcG
  3. E.5CM4: other-contacts is-WC-paired is-in-duplex [+]:GcG/cGC
  4. F.5CM13: stacking-with-D.ARG339 is-WC-paired is-in-duplex [-]:cGC/GcG
direct SNAP output · DNAproDB 2.0
Hashimoto, H., Wang, D., Horton, J.R., Zhang, X., Corces, V.G., Cheng, X.: (2017) "Structural Basis for the Versatile and Methylation-Dependent Binding of CTCF to DNA." Mol. Cell, 66, 711-720.e3.
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.

Base-block schematics in six views [summary · contacts · top · homepage · tutorial]

List of 4 5mC-amino acid contacts [summary · schematics · top · homepage · tutorial]

No. 1 B.5CM4: download PDB file for the 5mC entry
other-contacts is-WC-paired is-in-duplex [+]:GcG/cGC
No. 2 C.5CM13: download PDB file for the 5mC entry
stacking-with-A.ARG339 is-WC-paired is-in-duplex [-]:cGC/GcG
No. 3 E.5CM4: download PDB file for the 5mC entry
other-contacts is-WC-paired is-in-duplex [+]:GcG/cGC
No. 4 F.5CM13: download PDB file for the 5mC entry
stacking-with-D.ARG339 is-WC-paired is-in-duplex [-]:cGC/GcG