1QN8

Crystal structure of the T(-28) Adenovirus major late promoter TATA box variant bound to wild-type TBP (Arabidopsis thaliana TBP isoform 2). TATA element recognition by the TATA box-binding protein has been conserved throughout evolution.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

TATA Element Recognition by the TATA Box-Binding Protein Has Been Conserved Throughout Evolution

Patikoglou, G.A.Kim, J.L.Sun, L.Yang, S.-H.Kodadek, T.Burley, S.K.

(1999) Genes Dev. 13: 3217

  • DOI: 10.1101/gad.13.24.3217
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Cocrystal structures of wild-type TATA box-binding protein (TBP) recognizing 10 naturally occurring TATA elements have been determined at 2.3-1.8 A resolution, and compared with our 1.9 A resolution structure of TBP bound to the Adenovirus major late ...

    Cocrystal structures of wild-type TATA box-binding protein (TBP) recognizing 10 naturally occurring TATA elements have been determined at 2.3-1.8 A resolution, and compared with our 1.9 A resolution structure of TBP bound to the Adenovirus major late promoter (AdMLP) TATA box (5'-TATAAAAG-3'). Minor-groove recognition by the saddle-shaped protein induces the same conformational change in each of these oligonucleotides, despite variations in promoter sequence that reduce the efficiency of transcription initiation. Three molecular mechanisms explain assembly of diverse TBP-TATA element complexes. (1) T --> A and A --> T transversions leave the minor-groove face unchanged, permitting formation of TBP-DNA complexes on many A/T-rich core promoter sequences. (2) Cavities in the interface between TBP and the minor-groove face of the AdMLP TATA box accommodate the exocyclic NH(2) groups of G in a TACA box and in a TATAAG box. (3) Formation of a C:G Hoogsteen basepair in a TATAAAC box eliminates steric clashes that would be produced by the Watson-Crick base pair. We conclude that the structure of the TBP-TATA box complex found at the heart of the polymerase II (pol II) transcription machinery has remained constant over the course of evolution, despite variations in TBP and its DNA targets.


    Organizational Affiliation

    Laboratories of Molecular Biophysics, Howard Hughes Medical Institute, The Rockefeller University, New York, New York 10021 USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TRANSCRIPTION INITIATION FACTOR TFIID-1
A, B
200Arabidopsis thalianaMutation(s): 0 
Gene Names: TBP1
Find proteins for P28147 (Arabidopsis thaliana)
Go to UniProtKB:  P28147
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*CP*TP*AP*TP*TP*AP*AP*AP*GP*GP*GP*CP*A)-3')C,E14N/A
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*GP*CP*CP*CP*TP*TP*TP*AP*AP*TP*AP*GP*C)-3')D,F14N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.194 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 41.800α = 90.00
b = 146.700β = 90.50
c = 57.400γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
DENZOdata reduction
SCALEPACKdata scaling
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-02-07
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance