5HOD

Structure of LHX4 transcription factor complexed with DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.682 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.233 

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:  5EF6, 5EGO, 5LTY, 5LUX

  • 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
LIM/homeobox protein Lhx4
A, D
61Homo sapiensGene Names: LHX4
Find proteins for Q969G2 (Homo sapiens)
Go to Gene View: LHX4
Go to UniProtKB:  Q969G2
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(P*AP*CP*CP*TP*AP*AP*TP*TP*AP*GP*GP*CP*GP*TP*AP*AP*TP*TP*AP*G)-3')B20Homo sapiens
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(P*CP*TP*AP*AP*TP*TP*AP*CP*GP*CP*CP*TP*AP*AP*TP*TP*AP*GP*GP*T)-3')C20Homo sapiens
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.682 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.233 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 40.768α = 90.00
b = 68.442β = 90.00
c = 200.464γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
MOLREPphasing
XSCALEdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-02-01
    Type: Initial release
  • Version 1.1: 2017-05-17
    Type: Database references