6E16

Ternary structure of c-Myc-TBP-TAF1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • 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


This is version 1.2 of the entry. See complete history


Literature

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: 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 ...

    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. maria.sunnerhagen@liu.se.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 1,Myc proto-oncogene protein,TATA-box-binding proteinA267Saccharomyces cerevisiae S288CHomo sapiensMutation(s): 0 
Gene Names: 
EC: 2.3.1.48
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
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 GroupsP46677P01106P13393
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing

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