3WTT

Crystal structure of the complex comprised of phosphorylated ETS1, RUNX1, CBFBETA, and the tcralpha gene enhancer DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.241 

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
  • Structures With Same Primary Citation

  • 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. Electronic address: ogata@med.yokohama-cu.ac.jp.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Protein C-ets-1C, H166Homo sapiensMutation(s): 0 
Gene Names: ETS1EWSR2
Find proteins for P14921 (Homo sapiens)
Explore P14921 
Go to UniProtKB:  P14921
NIH Common Fund Data Resources
PHAROS  P14921
Protein Feature View
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Runt-related transcription factor 1A, F204Mus musculusMutation(s): 1 
Gene Names: Aml1Cbfa2Pebp2abRunx1
Find proteins for Q03347 (Mus musculus)
Explore Q03347 
Go to UniProtKB:  Q03347
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Core-binding factor subunit betaB, G142Mus musculusMutation(s): 0 
Gene Names: CbfbPebp2bPebpb2
Find proteins for Q08024 (Mus musculus)
Explore Q08024 
Go to UniProtKB:  Q08024
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 4
MoleculeChainsLengthOrganism
5'-D(*GP*AP*AP*GP*CP*CP*AP*CP*AP*TP*CP*CP*TP*CP*T)-3'D, I15N/A
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 5
MoleculeChainsLengthOrganism
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: 2.35 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.241 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.618α = 90
b = 101.718β = 90
c = 194.721γ = 90
Software Package:
Software NamePurpose
PHASERphasing
CNSrefinement
HKL-2000data reduction
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-08-13
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Refinement description