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 
  • R-Value Observed: 0.230 

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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: https://doi.org/10.1126/science.aaj2239
  • Primary Citation of Related Structures:  
    5EF6, 5EGO, 5HOD, 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 diminished by methylation of their target sequences ...

    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: 

    Genome-Scale Biology Program, Post Office Box 63, FI-00014 University of Helsinki, Helsinki, Finland.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Homeobox protein Meis1A57Homo sapiensMutation(s): 0 
Gene Names: MEIS1
UniProt & NIH Common Fund Data Resources
Find proteins for O00470 (Homo sapiens)
Explore O00470 
Go to UniProtKB:  O00470
PHAROS:  O00470
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00470
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Homeobox protein Hox-B13D [auth B]63Homo sapiensMutation(s): 0 
Gene Names: HOXB13
UniProt & NIH Common Fund Data Resources
Find proteins for Q92826 (Homo sapiens)
Explore Q92826 
Go to UniProtKB:  Q92826
PHAROS:  Q92826
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92826
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(P*GP*TP*TP*GP*AP*CP*AP*GP*TP*TP*TP*TP*AP*(5CM)P*GP*AP*GP*G)-3')B [auth D]18synthetic construct
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA (5'-D(*CP*CP*TP*(5CM)P*GP*TP*AP*AP*AP*AP*CP*TP*GP*TP*CP*AP*AP*C)-3')C [auth E]18synthetic construct
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.54 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.230 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.976α = 90
b = 51.48β = 90
c = 113.575γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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