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
- 5EF6
- Class
- transcription
- Method
- X-ray (3.0 Å)
- Summary
- Structure of hoxb13 complex with methylated DNA
List of 8 5mC-amino acid contacts:
-
C.5CM11: hydrophobic-with-A.ILE262 is-WC-paired is-in-duplex [+]:AcG/cGT
-
F.5CM7: hydrophobic-with-A.VAL269 is-WC-paired is-in-duplex [-]:cGA/TcG
-
D.5CM11: hydrophobic-with-B.ILE262 is-WC-paired is-in-duplex [+]:AcG/cGT
-
E.5CM7: hydrophobic-with-B.VAL269 is-WC-paired is-in-duplex [-]:cGG/CcG
-
H.5CM11: hydrophobic-with-G.ILE262 is-WC-paired is-in-duplex [+]:AcG/cGT
-
I.5CM7: hydrophobic-with-G.VAL269 is-WC-paired is-in-duplex [-]:cGG/CcG
-
K.5CM11: hydrophobic-with-J.ILE262 is-WC-paired is-in-duplex [+]:AcG/cGT
-
L.5CM7: hydrophobic-with-J.VAL269 is-WC-paired is-in-duplex [-]:cGG/CcG
direct SNAP output · DNAproDB 2.0
- Reference
- Yin, Y., Morgunova, E., Jolma, A., Kaasinen, E., Sahu, B., Khund-Sayeed, S., Das, P.K., Kivioja, T., Dave, K., Zhong, F., Nitta, K.R., Taipale, M., Popov, A., Ginno, P.A., Domcke, S., Yan, J., Schubeler, D., Vinson, C., Taipale, J.: (2017) "Impact of cytosine methylation on DNA binding specificities of human transcription factors." Science, 356
- Abstract
- The majority of CpG dinucleotides in the human genome are methylated at cytosine bases. However, active gene regulatory elements are generally hypomethylated relative to their flanking regions, and the binding of some transcription factors (TFs) is diminished by methylation of their target sequences. By analysis of 542 human TFs with methylation-sensitive SELEX (systematic evolution of ligands by exponential enrichment), we found that there are also many TFs that prefer CpG-methylated sequences. Most of these are in the extended homeodomain family. Structural analysis showed that homeodomain specificity for methylcytosine depends on direct hydrophobic interactions with the methylcytosine 5-methyl group. This study provides a systematic examination of the effect of an epigenetic DNA modification on human TF binding specificity and reveals that many developmentally important proteins display preference for mCpG-containing sequences.
- 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.
 |
No. 1 C.5CM11: download PDB file
for the 5mC entry
hydrophobic-with-A.ILE262 is-WC-paired is-in-duplex [+]:AcG/cGT
|
 |
No. 2 F.5CM7: download PDB file
for the 5mC entry
hydrophobic-with-A.VAL269 is-WC-paired is-in-duplex [-]:cGA/TcG
|
 |
No. 3 D.5CM11: download PDB file
for the 5mC entry
hydrophobic-with-B.ILE262 is-WC-paired is-in-duplex [+]:AcG/cGT
|
 |
No. 4 E.5CM7: download PDB file
for the 5mC entry
hydrophobic-with-B.VAL269 is-WC-paired is-in-duplex [-]:cGG/CcG
|
 |
No. 5 H.5CM11: download PDB file
for the 5mC entry
hydrophobic-with-G.ILE262 is-WC-paired is-in-duplex [+]:AcG/cGT
|
 |
No. 6 I.5CM7: download PDB file
for the 5mC entry
hydrophobic-with-G.VAL269 is-WC-paired is-in-duplex [-]:cGG/CcG
|
 |
No. 7 K.5CM11: download PDB file
for the 5mC entry
hydrophobic-with-J.ILE262 is-WC-paired is-in-duplex [+]:AcG/cGT
|
 |
No. 8 L.5CM7: download PDB file
for the 5mC entry
hydrophobic-with-J.VAL269 is-WC-paired is-in-duplex [-]:cGG/CcG
|
