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:  
    4XRM, 4XRS, 5BNG

  • 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 binding of multiple TFs to closely located motifs ...

    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

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Homeobox protein Meis2D [auth A],
A [auth B]		60Homo sapiensMutation(s): 0 
Gene Names: MEIS2, MRG1
UniProt & NIH Common Fund Data Resources
Find proteins for O14770 (Homo sapiens)
Explore O14770 
Go to UniProtKB:  O14770
PHAROS:  O14770
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO14770
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(P*TP*TP*AP*GP*CP*TP*GP*TP*CP*A)-3')B [auth L]10Homo sapiens
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Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA (5'-D(P*TP*GP*AP*CP*AP*GP*CP*TP*AP*A-3')C [auth M]12Homo sapiens
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  • Reference Sequence

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Entity ID: 4
MoleculeChainsLengthOrganismImage
DNA (5'-D(P*AP*AP*TP*TP*AP*GP*CP*TP*GP*TP*CP*A)-3')E [auth C]12Homo sapiens
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Entity ID: 5
MoleculeChainsLengthOrganismImage
DNA (5'-D(P*TP*GP*AP*CP*AP*GP*CP*TP*AP*A)-3')F [auth D]10Homo sapiens
Protein Feature View
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  • Reference Sequence
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

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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