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 1.4 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: https://doi.org/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. 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

    Department of Biosciences and Nutrition, Karolinska Institutet, SE 141 83, Sweden.


Macromolecules

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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Homeobox protein Meis1E [auth A],
F [auth B]
58Homo 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
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  • Reference Sequence
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Homeobox protein DLX-3G,
H [auth I]
56Homo sapiensMutation(s): 0 
Gene Names: DLX3
UniProt & NIH Common Fund Data Resources
Find proteins for O60479 (Homo sapiens)
Explore O60479 
Go to UniProtKB:  O60479
PHAROS:  O60479
GTEx:  ENSG00000064195 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60479
Sequence Annotations
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  • Reference Sequence

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Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(P*CP*AP*AP*TP*TP*AP*TP*CP*CP*TP*GP*TP*CP*AP*A)-3')A [auth M]15synthetic construct
Sequence Annotations
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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(P*AP*CP*AP*AP*TP*TP*AP*TP*CP*CP*TP*GP*TP*CP*AP*AP*C)-3')B [auth D]17synthetic construct
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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(P*GP*TP*TP*GP*AP*CP*AP*GP*GP*AP*TP*AP*AP*TP*TP*GP*TP*T)-3')C [auth E]18synthetic construct
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Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (5'-D(P*TP*TP*GP*AP*CP*AP*GP*GP*AP*TP*AP*AP*TP*TP*GP*T)-3')D [auth L]17synthetic construct
Sequence Annotations
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  • Reference Sequence
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

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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
  • Version 1.3: 2019-04-03
    Changes: Data collection, Source and taxonomy
  • Version 1.4: 2024-01-10
    Changes: Data collection, Database references, Refinement description