5BNG

monomer of TALE type homeobox transcription factor MEIS1 complexes with specific DNA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.388 
  • R-Value Work: 0.343 
  • R-Value Observed: 0.345 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

DNA-dependent formation of transcription factor pairs alters their binding specificity.

Jolma, A., Yin, Y., Nitta, K.R., Dave, K., Popov, A., Taipale, M., Enge, M., Kivioja, T., Morgunova, E., Taipale, J.

(2015) Nature 527: 384-388

  • DOI: 10.1038/nature15518
  • Primary Citation of Related Structures:  
    5BNG, 4XRM, 4XRS

  • PubMed Abstract: 

    • Gene expression is regulated by transcription factors (TFs), proteins that recognize short DNA sequence motifs. Such sequences are very common in the human genome, and an important determinant of the specificity of gene expression is the cooperative ...

    Gene expression is regulated by transcription factors (TFs), proteins that recognize short DNA sequence motifs. Such sequences are very common in the human genome, and an important determinant of the specificity of gene expression is the cooperative binding of multiple TFs to closely located motifs. However, interactions between DNA-bound TFs have not been systematically characterized. To identify TF pairs that bind cooperatively to DNA, and to characterize their spacing and orientation preferences, we have performed consecutive affinity-purification systematic evolution of ligands by exponential enrichment (CAP-SELEX) analysis of 9,400 TF-TF-DNA interactions. This analysis revealed 315 TF-TF interactions recognizing 618 heterodimeric motifs, most of which have not been previously described. The observed cooperativity occurred promiscuously between TFs from diverse structural families. Structural analysis of the TF pairs, including a novel crystal structure of MEIS1 and DLX3 bound to their identified recognition site, revealed that the interactions between the TFs were predominantly mediated by DNA. Most TF pair sites identified involved a large overlap between individual TF recognition motifs, and resulted in recognition of composite sites that were markedly different from the individual TF's motifs. Together, our results indicate that the DNA molecule commonly plays an active role in cooperative interactions that define the gene regulatory lexicon.

    Organizational Affiliation: 

    Genome-Scale Biology Program, University of Helsinki, P.O. Box 63, FI-00014, Finland.



Macromolecules

Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Homeobox protein Meis2A, B60Homo sapiensMutation(s): 0 
Gene Names: MEIS2, MRG1
Find proteins for O14770 (Homo sapiens)
Explore O14770 
Go to UniProtKB:  O14770
NIH Common Fund Data Resources
PHAROS  O14770
GTEx  ENSG00000134138
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(P*TP*TP*AP*GP*CP*TP*GP*TP*CP*A)-3')L10Homo sapiens
    • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(P*TP*GP*AP*CP*AP*GP*CP*TP*AP*A-3')M12Homo sapiens
      • Find similar nucleic acids by:  Sequence   |   Structure
        • Entity ID: 4
        MoleculeChainsLengthOrganismImage
        DNA (5'-D(P*AP*AP*TP*TP*AP*GP*CP*TP*GP*TP*CP*A)-3')C12Homo sapiens
        • Find similar nucleic acids by:  Sequence   |   Structure
          • Entity ID: 5
          MoleculeChainsLengthOrganismImage
          DNA (5'-D(P*TP*GP*AP*CP*AP*GP*CP*TP*AP*A)-3')D10Homo sapiens
          Experimental Data & Validation

          Experimental Data

          • Method: X-RAY DIFFRACTION
          • Resolution: 3.50 Å
          • R-Value Free: 0.388 
          • R-Value Work: 0.343 
          • R-Value Observed: 0.345 
          • Space Group: P 21 21 21
          Unit Cell:
          Length ( Å )Angle ( ˚ )
          a = 45.9α = 90
          b = 59.94β = 90
          c = 107.94γ = 90
          Software Package:
          Software NamePurpose
          XDSdata reduction
          SCALAdata scaling
          PHASERphasing
          PHENIXrefinement
          PDB_EXTRACTdata extraction

          Structure Validation

          View Full Validation Report


          View more in-depth experimental data

          Entry History 

          Deposition Data

          Revision History 

          • Version 1.0: 2015-11-04
            Type: Initial release
          • Version 1.1: 2015-11-18
            Changes: Database references
          • Version 1.2: 2015-12-02
            Changes: Database references