4OV7

Ancestral Steroid Receptor 2 DBD helix mutant - SRE DNA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.701 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Evolution of DNA specificity in a transcription factor family produced a new gene regulatory module.

McKeown, A.N.Bridgham, J.T.Anderson, D.W.Murphy, M.N.Ortlund, E.A.Thornton, J.W.

(2014) Cell 159: 58-68

  • DOI: 10.1016/j.cell.2014.09.003
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Complex gene regulatory networks require transcription factors (TFs) to bind distinct DNA sequences. To understand how novel TF specificity evolves, we combined phylogenetic, biochemical, and biophysical approaches to interrogate how DNA recognition ...

    Complex gene regulatory networks require transcription factors (TFs) to bind distinct DNA sequences. To understand how novel TF specificity evolves, we combined phylogenetic, biochemical, and biophysical approaches to interrogate how DNA recognition diversified in the steroid hormone receptor (SR) family. After duplication of the ancestral SR, three mutations in one copy radically weakened binding to the ancestral estrogen response element (ERE) and improved binding to a new set of DNA sequences (steroid response elements, SREs). They did so by establishing unfavorable interactions with ERE and abolishing unfavorable interactions with SRE; also required were numerous permissive substitutions, which nonspecifically improved cooperativity and affinity of DNA binding. Our findings indicate that negative determinants of binding play key roles in TFs' DNA selectivity and-with our prior work on the evolution of SR ligand specificity during the same interval-show how a specific new gene regulatory module evolved without interfering with the integrity of the ancestral module.


    Organizational Affiliation

    Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ancestral Steroid Receptor 2 DBD helix mutant
A, B, E, F
82N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*CP*CP*AP*GP*AP*AP*CP*AP*GP*AP*GP*TP*GP*TP*TP*CP*TP*G)-3'I,K18N/A
Entity ID: 3
MoleculeChainsLengthOrganism
5'-D(*TP*CP*AP*GP*AP*AP*CP*AP*CP*TP*CP*TP*GP*TP*TP*CP*TP*G)-3'J,L18N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, E, F
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.701 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.199 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 47.472α = 90.00
b = 80.374β = 96.74
c = 115.645γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
PHASERphasing
DENZOdata reduction
PHENIXrefinement
SERGUIdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2014-02-20 
  • Released Date: 2014-10-29 
  • Deposition Author(s): Ortlund, E.A.

Revision History 

  • Version 1.0: 2014-10-29
    Type: Initial release
  • Version 1.1: 2017-11-22
    Type: Refinement description