4YO2

Structure of E2F8, an atypical member of E2F family of transcription factors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.07 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.272 
  • R-Value Observed: 0.272 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural insights into the DNA-binding specificity of E2F family transcription factors.

Morgunova, E.Yin, Y.Jolma, A.Dave, K.Schmierer, B.Popov, A.Eremina, N.Nilsson, L.Taipale, J.

(2015) Nat Commun 6: 10050-10050

  • DOI: https://doi.org/10.1038/ncomms10050
  • Primary Citation of Related Structures:  
    4YO2

  • PubMed Abstract: 

    The mammalian cell cycle is controlled by the E2F family of transcription factors. Typical E2Fs bind to DNA as heterodimers with the related dimerization partner (DP) proteins, whereas the atypical E2Fs, E2F7 and E2F8 contain two DNA-binding domains (DBDs) and act as repressors. To understand the mechanism of repression, we have resolved the structure of E2F8 in complex with DNA at atomic resolution. We find that the first and second DBDs of E2F8 resemble the DBDs of typical E2F and DP proteins, respectively. Using molecular dynamics simulations, biochemical affinity measurements and chromatin immunoprecipitation, we further show that both atypical and typical E2Fs bind to similar DNA sequences in vitro and in vivo. Our results represent the first crystal structure of an E2F protein with two DBDs, and reveal the mechanism by which atypical E2Fs can repress canonical E2F target genes and exert their negative influence on cell cycle progression.


  • Organizational Affiliation

    Department of Biosciences and Nutrition, Karolinska Institutet, SE 141 83 Stockholm, Sweden.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription factor E2F8232Homo sapiensMutation(s): 0 
Gene Names: E2F8
UniProt & NIH Common Fund Data Resources
Find proteins for A0AVK6 (Homo sapiens)
Explore A0AVK6 
Go to UniProtKB:  A0AVK6
PHAROS:  A0AVK6
GTEx:  ENSG00000129173 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0AVK6
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(P*TP*TP*TP*TP*CP*CP*CP*GP*CP*CP*AP*AP*AP*AP*A)-3')B [auth C]15Homo sapiens
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(P*TP*TP*TP*TP*TP*GP*GP*CP*GP*GP*GP*AP*AP*AP*A)-3')C [auth D]15Homo sapiens
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.07 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.272 
  • R-Value Observed: 0.272 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.83α = 90
b = 98.83β = 90
c = 121.69γ = 120
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
XSCALEdata scaling
Cootmodel building
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-12-09
    Type: Initial release
  • Version 1.1: 2015-12-16
    Changes: Database references
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Refinement description