1TBP | pdb_00001tbp

CRYSTAL STRUCTURE OF YEAST TATA-BINDING PROTEIN AND MODEL FOR INTERACTION WITH DNA

• PDB DOI: https://doi.org/10.2210/pdb1TBP/pdb

• Classification: BINDING PROTEIN
• Organism(s): Saccharomyces cerevisiae
• Mutation(s): No 


• Deposited: 1993-08-02 Released: 1994-01-31 
• Deposition Author(s): Chasman, D.I., Flaherty, K.M., Sharp, P.A., Kornberg, R.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Work: 
  0.211 (Depositor) 
• R-Value Observed: 
  0.211 (Depositor) 

Literature

Crystal structure of yeast TATA-binding protein and model for interaction with DNA.

Chasman, D.I., Flaherty, K.M., Sharp, P.A., Kornberg, R.D.

(1993) Proc Natl Acad Sci U S A 90: 8174-8178

• PubMed: 8367480 
• DOI: https://doi.org/10.1073/pnas.90.17.8174
• Primary Citation Related Structures: 
  1TBP


• PubMed Abstract: 
  

  The C-terminal 179-aa region of yeast (Saccharomyces cerevisiae) TATA-binding protein (TBP), phylogenetically conserved and sufficient for many functions, formed crystals diffracting to 1.7-A resolution. The structure of the protein, determined by molecular replacement with coordinates from Arabidopsis TBP and refined to 2.6 A, differed from that in Arabidopsis slightly by an angle of about 12 degrees between two structurally nearly identical subdomains, indicative of a degree of conformational flexibility. A model for TBP-DNA interaction is proposed with the following important features: the long dimension of the protein follows the trajectory of the minor groove; two rows of basic residues conserved between the subdomains lie along the edges of the protein in proximity to the DNA phosphates; a band of hydrophobic residues runs down the middle of the groove; and amino acid residues whose mutation alters specificity for the second base of the TATA sequence are juxtaposed to that base.

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Organizational Affiliation: 
• Center for Cancer Research, Massachusetts Institute of Technology, Cambridge 02139.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 40.33 kDa 
• Atom Count: 2,834 
• Modeled Residue Count: 360 
• Deposited Residue Count: 360 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TATA-BINDING PROTEIN	A, B	180	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P13393 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P13393  Go to UniProtKB:  P13393

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Work:  0.211 (Depositor) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.1	α = 90
b = 104.1	β = 90
c = 75.5	γ = 120

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1994-01-31 
Deposition Author(s): Chasman, D.I., Flaherty, K.M., Sharp, P.A., Kornberg, R.D.

Revision History  

• Version 1.0: 1994-01-31
  Type: Initial release
  
• Version 1.1: 2008-03-24
  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, Other