1VTL

CO-CRYSTAL STRUCTURE OF TBP RECOGNIZING THE MINOR GROOVE OF A TATA ELEMENT

• PDB DOI: https://doi.org/10.2210/pdb1VTL/pdb
• NAKB: 1VTL

• Classification: TRANSCRIPTION/DNA
• Organism(s): Arabidopsis thaliana
• Mutation(s): No 


• Deposited: 1993-12-17 Released: 2011-07-13 
• Deposition Author(s): Kim, J.L., Nikolov, D.B., Burley, S.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Work: 0.202 
• R-Value Observed: 0.202 

Literature

Co-Crystal Structure of TBP Recognizing the Minor Groove of a TATA Element

Kim, J.L., Nikolov, D.B., Burley, S.K.

(1993) Nature 365: 520-527

• PubMed: 8413605 
• DOI: https://doi.org/10.1038/365520a0
• Primary Citation of Related Structures:  
  1VTL


• PubMed Abstract: 
  

  The three-dimensional structure of a TATA-box binding polypeptide complexed with the TATA element of the adenovirus major late promoter has been determined by X-ray crystallography at 2.25 A resolution. Binding of the saddle-shaped protein induces a conformational change in the DNA, inducing sharp kinks at either end of the sequence TATAAAAG. Between the kinks, the right-handed double helix is smoothly curved and partially unwound, presenting a widened minor groove to TBP's concave, antiparallel beta-sheet. Side-chain/base interactions are restricted to the minor groove, and include hydrogen bonds, van der Waals contacts and phenylalanine-base stacking interactions.

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Organizational Affiliation: 

Laboratory of Molecular Biophysics, Rockefeller University, New York, New York 10021.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 58.95 kDa 
• Atom Count: 4,057 
• Modelled Residue Count: 428 
• Deposited Residue Count: 428 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
TATA BINDING PROTEIN (TBP)	E, F	186	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for P28147 (Arabidopsis thaliana) Explore P28147  Go to UniProtKB:  P28147

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*CP*TP*AP*TP*AP*AP*AP*AP*GP*GP*GP*CP*A)-3')	A, C	14	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*GP*CP*CP*CP*TP*TP*TP*TP*AP*TP*AP*GP*C)-3')	B, D	14	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Work: 0.202 
• R-Value Observed: 0.202 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.8	α = 90
b = 146.5	β = 90.6
c = 57.6	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-07-13 
Deposition Author(s): Kim, J.L., Nikolov, D.B., Burley, S.K.

Revision History  

• Version 1.0: 2011-07-13
  Type: Initial release
  
• Version 1.1: 2021-02-03
  Changes: Database references, Structure summary
• Version 1.2: 2023-12-27
  Changes: Data collection, Database references