1YTB

CRYSTAL STRUCTURE OF A YEAST TBP/TATA-BOX COMPLEX

• PDB DOI: https://doi.org/10.2210/pdb1YTB/pdb
• NAKB: 1YTB

• Classification: TRANSCRIPTION/DNA
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1994-09-28 Released: 1995-01-26 
• Deposition Author(s): Kim, Y., Geiger, J.H., Hahn, S., Sigler, P.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.261 
• R-Value Work: 0.201 
• R-Value Observed: 0.201 

Literature

Crystal structure of a yeast TBP/TATA-box complex.

Kim, Y., Geiger, J.H., Hahn, S., Sigler, P.B.

(1993) Nature 365: 512-520

• PubMed: 8413604 
• DOI: https://doi.org/10.1038/365512a0
• Primary Citation of Related Structures:  
  1YTB


• PubMed Abstract: 
  

  The 2.5 A crystal structure of a TATA-box complex with yeast TBP shows that the eight base pairs of the TATA box bind to the concave surface of TBP by bending towards the major groove with unprecedented severity. This produces a wide open, underwound, shallow minor groove which forms a primarily hydrophobic interface with the entire under-surface of the TBP saddle. The severe bend and a positive writhe radically alter the trajectory of the flanking B-form DNA.

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Organizational Affiliation: 

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06510.

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: 58.22 kDa 
• Atom Count: 4,539 
• Modelled Residue Count: 418 
• Deposited Residue Count: 418 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (TATA BINDING PROTEIN (TBP))	C [auth A], D [auth B]	180	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P13393 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P13393  Go to UniProtKB:  P13393

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (29MER)	A [auth C], B [auth D]	29	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.261 
• R-Value Work: 0.201 
• R-Value Observed: 0.201 
• Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.77	α = 90
b = 100.77	β = 90
c = 66.5	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1995-01-26 
Deposition Author(s): Kim, Y., Geiger, J.H., Hahn, S., Sigler, P.B.

Revision History  

• Version 1.0: 1995-01-26
  Type: Initial release
  
• Version 1.1: 2008-05-22
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references