4XRS

Heterodimeric complex of transcription factors MEIS1 and DLX3 on specific DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.359 
  • R-Value Work: 0.331 
  • R-Value Observed: 0.343 

wwPDB Validation 3D Report Full Report


This is version 1.3 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: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Homeobox protein Meis1AB58Homo sapiensMutation(s): 0 
Gene Names: MEIS1
Find proteins for O00470 (Homo sapiens)
Explore O00470 
Go to UniProtKB:  O00470
NIH Common Fund Data Resources
PHAROS  O00470
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  • Reference Sequence
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Homeobox protein DLX-3GI56Homo sapiensMutation(s): 0 
Gene Names: DLX3
Find proteins for O60479 (Homo sapiens)
Explore O60479 
Go to UniProtKB:  O60479
NIH Common Fund Data Resources
PHAROS  O60479
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(P*CP*AP*AP*TP*TP*AP*TP*CP*CP*TP*GP*TP*CP*AP*A)-3')M15synthetic construct
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(P*AP*CP*AP*AP*TP*TP*AP*TP*CP*CP*TP*GP*TP*CP*AP*AP*C)-3')D17synthetic construct
      • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 3
        MoleculeChainsLengthOrganismImage
        DNA (5'-D(P*GP*TP*TP*GP*AP*CP*AP*GP*GP*AP*TP*AP*AP*TP*TP*GP*TP*T)-3')E18synthetic construct
        • Find similar nucleic acids by:  Sequence   |   Structure
        • Entity ID: 4
          MoleculeChainsLengthOrganismImage
          DNA (5'-D(P*TP*TP*GP*AP*CP*AP*GP*GP*AP*TP*AP*AP*TP*TP*GP*T)-3')L17synthetic construct
          Experimental Data & Validation

          Experimental Data

          • Method: X-RAY DIFFRACTION
          • Resolution: 3.50 Å
          • R-Value Free: 0.359 
          • R-Value Work: 0.331 
          • R-Value Observed: 0.343 
          • Space Group: P 21 21 21
          Unit Cell:
          Length ( Å )Angle ( ˚ )
          a = 69.636α = 90
          b = 69.845β = 90
          c = 116.888γ = 90
          Software Package:
          Software NamePurpose
          PHENIXrefinement
          SCALAdata scaling
          PHASERphasing
          PDB_EXTRACTdata extraction
          XDSdata reduction

          Structure Validation

          View Full Validation Report



          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
          • Version 1.3: 2019-04-03
            Changes: Data collection, Source and taxonomy