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 

wwPDB Validation   3D Report Full Report


This is version 1.2 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. 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Homeobox protein Meis157Homo 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
GTEx:  ENSG00000143995 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00470
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence 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
GTEx:  ENSG00000159184 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92826
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
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
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains LengthOrganismImage
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
Sequence Annotations
Expand
  • 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

View Full Validation Report



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
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Refinement description