Last updated on 2019-09-30 by Xiang-Jun Lu <xiangjun@x3dna.org>.
The block schematics were created with DSSR and
rendered using PyMOL.
- PDB-id
- 5T00
- Class
- transcription regulator-DNA
- Method
- X-ray (2.19 Å)
- Summary
- Human ctcf znf3-7 and methylated DNA complex
List of 4 5mC-amino acid contacts:
-
B.5CM4: other-contacts is-WC-paired is-in-duplex [+]:GcG/cGC
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C.5CM13: stacking-with-A.ARG339 is-WC-paired is-in-duplex [-]:cGC/GcG
-
E.5CM4: other-contacts is-WC-paired is-in-duplex [+]:GcG/cGC
-
F.5CM13: stacking-with-D.ARG339 is-WC-paired is-in-duplex [-]:cGC/GcG
direct SNAP output · DNAproDB 2.0
- Reference
- 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.
- 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 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.
- The 5-methylcytosine group (PDB ligand '5CM') is shown in space-filling model,
with the methyl-carbon atom in black.
- Watson-Crick base pairs are represented as long rectangular blocks with the
minor-groove edge in black. Color code: A-T red, C-G yellow, G-C green, T-A blue.
- Protein is shown as cartoon in purple. DNA backbones are shown ribbon, colored code
by chain identifier.
- The block schematics were created with 3DNA-DSSR,
and images were rendered using PyMOL.
- Download the PyMOL session file corresponding to the top-left
image in the following panel.
- The contacts include paired nucleotides (mostly a G in G-C pairing), and
amino-acids within a 4.5-A distance cutoff to the base atoms of 5mC.
- The structure is oriented in the 'standard' base reference frame of 5mC, allowing for easy comparison
and direct superimposition between entries.
- The black sphere (•) denotes the 5-methyl carbon atom in 5mC.
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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
|
