3WTW

Crystal structure of the complex comprised of ETS1(K167A), RUNX1, CBFBETA, and the tcralpha gene enhancer DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A novel allosteric mechanism on protein-DNA interactions underlying the phosphorylation-dependent regulation of Ets1 target gene expressions

Shiina, M.Hamada, K.Inoue-Bungo, T.Shimamura, M.Uchiyama, A.Baba, S.Sato, K.Yamamoto, M.Ogata, K.

(2014) J.Mol.Biol. --: --

  • DOI: 10.1016/j.jmb.2014.07.020
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Cooperative assemblies of transcription factors (TFs) on target gene enhancers coordinate cell proliferation, fate specification, and differentiation through precise and complicated transcriptional mechanisms. Chemical modifications, such as phosphor ...

    Cooperative assemblies of transcription factors (TFs) on target gene enhancers coordinate cell proliferation, fate specification, and differentiation through precise and complicated transcriptional mechanisms. Chemical modifications, such as phosphorylation, of TFs induced by cell signaling further modulate the dynamic cooperativity of TFs. In this study, we found that various Ets1-containing TF-DNA complexes respond differently to calcium-induced phosphorylation of Ets1, which is known to inhibit Ets1-DNA binding. Crystallographic analysis of a complex comprising Ets1, Runx1, and CBFβ at the TCRα enhancer revealed that Ets1 acquires robust binding stability in the Runx1 and DNA-complexed state, via allosteric mechanisms. This allows phosphorylated Ets1 to be retained at the TCRα enhancer with Runx1, in contrast to other Ets1 target gene enhancers including mb-1 and stromelysin-1. This study provides a structure-based model for cell-signaling-dependent regulation of target genes, mediated via chemical modification of TFs.


    Organizational Affiliation

    Department of Biochemistry, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama 236-0004, Japan; RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Runt-related transcription factor 1
A, F
204Mus musculusMutation(s): 2 
Gene Names: Runx1 (Aml1, Cbfa2, Pebp2ab)
Find proteins for Q03347 (Mus musculus)
Go to UniProtKB:  Q03347
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Core-binding factor subunit beta
B, G
142Mus musculusMutation(s): 0 
Gene Names: Cbfb (Pebp2b, Pebpb2)
Find proteins for Q08024 (Mus musculus)
Go to UniProtKB:  Q08024
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Protein C-ets-1
C, H
166Homo sapiensMutation(s): 0 
Gene Names: ETS1 (EWSR2)
Find proteins for P14921 (Homo sapiens)
Go to Gene View: ETS1
Go to UniProtKB:  P14921
Entity ID: 4
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*AP*AP*GP*CP*CP*AP*CP*AP*TP*CP*CP*TP*CP*T)-3')D,I15N/A
Entity ID: 5
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*GP*AP*GP*GP*AP*TP*GP*TP*GP*GP*CP*TP*TP*C)-3')E,J15N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.219 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 78.499α = 90.00
b = 100.613β = 90.00
c = 194.396γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-08-20
    Type: Initial release
  • Version 1.1: 2017-11-22
    Type: Refinement description