5EDN | pdb_00005edn

Structure of HOXB13-DNA(TCG) complex

• PDB DOI: https://doi.org/10.2210/pdb5EDN/pdb
• NAKB: 5EDN

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-10-21 Released: 2016-11-09 
• Deposition Author(s): Morgunova, E., Yin, Y., Jolma, A., Popov, A., Taipale, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 
  0.281 (Depositor), 0.279 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.215 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Starting Model: experimental

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

• PubMed: 29638214 
• DOI: https://doi.org/10.7554/eLife.32963
• Primary Citation Related Structures: 
  5EDN, 5EEA, 6ES2, 6ES3


• 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 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.

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Organizational Affiliation: 
• Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
Genome-Scale Biology Research Program, University of Helsinki, Helsinki, Finland.
European Synchrotron Radiation Facility, Grenoble, France.
Department of Bioscience and Nutrition, Karolinska Institutet, Huddinge, Sweden.
Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 82.68 kDa 
• Atom Count: 5,197 
• Modeled Residue Count: 394 
• Deposited Residue Count: 456 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Homeobox protein Hox-B13	A, B, G, J	76	Homo sapiens	Mutation(s): 0  Gene Names: HOXB13
UniProt & NIH Common Fund Data Resources
Find proteins for Q92826 (Homo sapiens) Explore Q92826  Go to UniProtKB:  Q92826
PHAROS:  Q92826 GTEx:  ENSG00000159184

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*GP*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*CP*GP*AP*GP*GP*TP*CP*C)-3')	C, D, H, K	19	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*GP*GP*AP*CP*CP*TP*CP*GP*TP*AP*AP*AP*AP*CP*AP*CP*AP*AP*C)-3')	E, F, I, L	19	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	M [auth C]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free:  0.281 (Depositor), 0.279 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.215 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.618	α = 90
b = 52.522	β = 90
c = 389.331	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-11-09 
Deposition Author(s): Morgunova, E., Yin, Y., Jolma, A., Popov, A., Taipale, J.

Revision History  

• Version 1.0: 2016-11-09
  Type: Initial release
  
• Version 1.1: 2018-08-15
  Changes: Data collection, Database references
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Refinement description