5mC interactions in PDB entry 4X9J 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 (1.41 Å)
Egr-1 with doubly methylated DNA
List of 4 5mC-amino acid contacts:
  1. B.5CM3: stacking-with-A.ARG174 is-WC-paired is-in-duplex [+]:GcG/cGC
  2. B.5CM9: stacking-with-A.ARG118 is-WC-paired is-in-duplex [+]:GcG/cGC
  3. C.5CM53: other-contacts is-WC-paired is-in-duplex [-]:cGT/AcG
  4. C.5CM59: other-contacts is-WC-paired is-in-duplex [-]:cGT/AcG
direct SNAP output · DNAproDB 2.0
Zandarashvili, L., White, M.A., Esadze, A., Iwahara, J.: (2015) "Structural impact of complete CpG methylation within target DNA on specific complex formation of the inducible transcription factor Egr-1." Febs Lett., 589, 1748-1753.
The inducible transcription factor Egr-1 binds specifically to 9-bp target sequences containing two CpG sites that can potentially be methylated at four cytosine bases. Although it appears that complete CpG methylation would make an unfavorable steric clash in the previous crystal structures of the complexes with unmethylated or partially methylated DNA, our affinity data suggest that DNA recognition by Egr-1 is insensitive to CpG methylation. We have determined, at a 1.4-Å resolution, the crystal structure of the Egr-1 zinc-finger complex with completely methylated target DNA. Structural comparison of the three different methylation states reveals why Egr-1 can recognize the target sequences regardless of CpG methylation.

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.5CM3: download PDB file for the 5mC entry
stacking-with-A.ARG174 is-WC-paired is-in-duplex [+]:GcG/cGC
No. 2 B.5CM9: download PDB file for the 5mC entry
stacking-with-A.ARG118 is-WC-paired is-in-duplex [+]:GcG/cGC
No. 3 C.5CM53: download PDB file for the 5mC entry
other-contacts is-WC-paired is-in-duplex [-]:cGT/AcG
No. 4 C.5CM59: download PDB file for the 5mC entry
other-contacts is-WC-paired is-in-duplex [-]:cGT/AcG