5EGO

HOXB13-MEIS1 heterodimer bound to methylated DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.54 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.228 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Impact of cytosine methylation on DNA binding specificities of human transcription factors.

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) Science 356: --

  • DOI: 10.1126/science.aaj2239
  • Primary Citation of Related Structures:  

  • PubMed 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 d ...

    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.


    Organizational Affiliation

    Division of Functional Genomics and Systems Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE 141 83 Stockholm, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Homeobox protein Meis1
A
57Homo sapiensMutation(s): 0 
Gene Names: MEIS1
Find proteins for O00470 (Homo sapiens)
Go to Gene View: MEIS1
Go to UniProtKB:  O00470
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Homeobox protein Hox-B13
B
63Homo sapiensMutation(s): 0 
Gene Names: HOXB13
Find proteins for Q92826 (Homo sapiens)
Go to Gene View: HOXB13
Go to UniProtKB:  Q92826
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(P*GP*TP*TP*GP*AP*CP*AP*GP*TP*TP*TP*TP*AP*(5CM)P*GP*AP*GP*G)-3')D18synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*CP*TP*(5CM)P*GP*TP*AP*AP*AP*AP*CP*TP*GP*TP*CP*AP*AP*C)-3')E18synthetic construct
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
5CM
Query on 5CM
D, E
DNA LINKINGC10 H16 N3 O7 PDC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.54 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.228 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 40.976α = 90.00
b = 51.480β = 90.00
c = 113.575γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
PHASERphasing
Aimlessdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-11-09
    Type: Initial release
  • Version 1.1: 2017-05-17
    Type: Database references