1QNC

Crystal structure of the A(-31) 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: 2.30 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.182 

wwPDB Validation   3D Report Full Report


This is version 1.3 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:  
    1QN3, 1QN4, 1QN5, 1QN6, 1QN7, 1QN8, 1QN9, 1QNA, 1QNB, 1QNC, 1QNE

  • 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 promoter (AdMLP) TATA box (5'-TATAAAAG-3') ...

    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

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TRANSCRIPTION INITIATION FACTOR TFIID-1A, B200Arabidopsis thalianaMutation(s): 0 
Gene Names: TBP1, At3g13445, MRP15.10
UniProt
Find proteins for P28147 (Arabidopsis thaliana)
Explore P28147 
Go to UniProtKB:  P28147
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28147
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(*GP*CP*AP*AP*TP*AP*AP*AP*AP*GP*GP*GP*CP*A)-3')C, E 14N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA (5'-D(*TP*GP*CP*CP*CP*TP*TP*TP*TP*AP*TP*TP*GP*C)-3')D, F 14N/A
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.182 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42α = 90
b = 57β = 96
c = 147γ = 90
Software Package:
Software NamePurpose
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-02-07
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-02-03
    Changes: Database references, Structure summary