6ES3

Structure of CDX2-DNA(TCG)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.216 

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: 2
MoleculeChainsSequence LengthOrganismDetails
Homeobox protein CDX-2
K, M
72Homo sapiensMutation(s): 0 
Gene Names: CDX2 (CDX3)
Find proteins for Q99626 (Homo sapiens)
Go to Gene View: CDX2
Go to UniProtKB:  Q99626
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*CP*GP*AP*CP*CP*TP*CP*C)-3')A,B18Homo sapiens
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(P*GP*GP*AP*GP*GP*TP*CP*GP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3')F,E18Homo sapiens
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.216 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 127.950α = 90.00
b = 46.490β = 113.27
c = 68.890γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-03-21
    Type: Initial release
  • Version 1.1: 2018-05-16
    Type: Data collection, Database references