5EEA

Structure of HOXB13-DNA(CAA) complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.195 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.251 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Two distinct DNA sequences recognized by transcription factors represent enthalpy and entropy optima.

Morgunova, E.Yin, Y.Das, P.K.Jolma, A.Zhu, F.Popov, A.Xu, Y.Nilsson, L.Taipale, J.

(2018) Elife 7: --

  • DOI: 10.7554/eLife.32963
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Most transcription factors (TFs) can bind to a population of sequences closely related to a single optimal site. However, some TFs can bind to two distinct sequences that represent two local optima in the Gibbs free energy of binding (ΔG). To determi ...

    Most transcription factors (TFs) can bind to a population of sequences closely related to a single optimal site. However, some TFs can bind to two distinct sequences that represent two local optima in the Gibbs free energy of binding (ΔG). To determine the molecular mechanism behind this effect, we solved the structures of human HOXB13 and CDX2 bound to their two optimal DNA sequences, CAATAAA and TCGTAAA. Thermodynamic analyses by isothermal titration calorimetry revealed that both sites were bound with similar ΔG. However, the interaction with the CAA sequence was driven by change in enthalpy (ΔH), whereas the TCG site was bound with similar affinity due to smaller loss of entropy (ΔS). This thermodynamic mechanism that leads to at least two local optima likely affects many macromolecular interactions, as ΔG depends on two partially independent variables ΔH and ΔS according to the central equation of thermodynamics, ΔG = ΔH - TΔS.


    Organizational Affiliation

    Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Homeobox protein Hox-B13
B, A, G, J
63Homo sapiensMutation(s): 0 
Gene Names: HOXB13
Find proteins for Q92826 (Homo sapiens)
Go to Gene View: HOXB13
Go to UniProtKB:  Q92826
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*TP*TP*GP*GP*GP*TP*CP*C)-3')D,C,H,K18synthetic construct
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(P*GP*GP*AP*CP*CP*CP*AP*AP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3')E,F,I,L18synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.195 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.251 
  • Space Group: P 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 77.356α = 90.00
b = 57.918β = 101.57
c = 101.278γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
SCALAdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-10-26
    Type: Initial release
  • Version 1.1: 2018-08-15
    Type: Data collection, Database references