Ternary structure of c-Myc-TBP-TAF1

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 

wwPDB Validation   3D Report Full Report

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Multiple direct interactions of TBP with the MYC oncoprotein.

Wei, Y.Resetca, D.Li, Z.Johansson-Akhe, I.Ahlner, A.Helander, S.Wallenhammar, A.Morad, V.Raught, B.Wallner, B.Kokubo, T.Tong, Y.Penn, L.Z.Sunnerhagen, M.

(2019) Nat Struct Mol Biol 26: 1035-1043

  • DOI: https://doi.org/10.1038/s41594-019-0321-z
  • Primary Citation of Related Structures:  
    6E16, 6E24

  • PubMed Abstract: 

    Transcription factor c-MYC is a potent oncoprotein; however, the mechanism of transcriptional regulation via MYC-protein interactions remains poorly understood. The TATA-binding protein (TBP) is an essential component of the transcription initiation complex TFIID and is required for gene expression. We identify two discrete regions mediating MYC-TBP interactions using structural, biochemical and cellular approaches. A 2.4 -Å resolution crystal structure reveals that human MYC amino acids 98-111 interact with TBP in the presence of the amino-terminal domain 1 of TBP-associated factor 1 (TAF1 TAND1 ). Using biochemical approaches, we have shown that MYC amino acids 115-124 also interact with TBP independently of TAF1 TAND1 . Modeling reveals that this region of MYC resembles a TBP anchor motif found in factors that regulate TBP promoter loading. Site-specific MYC mutants that abrogate MYC-TBP interaction compromise MYC activity. We propose that MYC-TBP interactions propagate transcription by modulating the energetic landscape of transcription initiation complex assembly.

  • Organizational Affiliation

    Department of Physics, Chemistry, and Biology, Linköping University, Linköping, Sweden.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 1,Myc proto-oncogene protein,TATA-box-binding protein267Saccharomyces cerevisiae S288CHomo sapiensMutation(s): 0 
Gene Names: 
UniProt & NIH Common Fund Data Resources
Find proteins for P13393 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P13393 
Go to UniProtKB:  P13393
Find proteins for P01106 (Homo sapiens)
Explore P01106 
Go to UniProtKB:  P01106
PHAROS:  P01106
GTEx:  ENSG00000136997 
Find proteins for P46677 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P46677 
Go to UniProtKB:  P46677
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP13393P01106P46677
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.816α = 90
b = 72.816β = 90
c = 78.819γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-02
    Type: Initial release
  • Version 1.1: 2019-11-20
    Changes: Database references
  • Version 1.2: 2019-11-27
    Changes: Database references