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
  • Structures With Same Primary Citation

  • 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: Sequence  |  Structure

Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Homeobox protein Meis1
A, B
58Homo sapiensMutation(s): 0 
Gene Names: MEIS1
Find proteins for O00470 (Homo sapiens)
Go to UniProtKB:  O00470
NIH Common Fund Data Resources
PHAROS  O00470

Find similar proteins by: Sequence  |  Structure

Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Homeobox protein DLX-3
G, I
56Homo sapiensMutation(s): 0 
Gene Names: DLX3
Find proteins for O60479 (Homo sapiens)
Go to UniProtKB:  O60479
NIH Common Fund Data Resources
PHAROS  O60479
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 1
MoleculeChainsLengthOrganism
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: 3
MoleculeChainsLengthOrganism
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
MoleculeChainsLengthOrganism
DNA (5'-D(P*TP*TP*GP*AP*CP*AP*GP*GP*AP*TP*AP*AP*TP*TP*GP*T)-3')L17synthetic construct
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(P*AP*CP*AP*AP*TP*TP*AP*TP*CP*CP*TP*GP*TP*CP*AP*AP*C)-3')D17synthetic 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