1D3U | pdb_00001d3u

TATA-BINDING PROTEIN/TRANSCRIPTION FACTOR (II)B/BRE+TATA-BOX COMPLEX FROM PYROCOCCUS WOESEI

• PDB DOI: https://doi.org/10.2210/pdb1D3U/pdb
• NAKB: 1D3U

• Classification: GENE REGULATION/DNA
• Organism(s): Pyrococcus woesei
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 1999-10-01 Released: 1999-11-15 
• Deposition Author(s): Littlefield, O., Korkhin, Y., Sigler, P.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.245 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.212 (Depositor) 

Literature

The structural basis for the oriented assembly of a TBP/TFB/promoter complex.

Littlefield, O., Korkhin, Y., Sigler, P.B.

(1999) Proc Natl Acad Sci U S A 96: 13668-13673

• PubMed: 10570130 
• DOI: https://doi.org/10.1073/pnas.96.24.13668
• Primary Citation of Related Structures:  
  1D3U


• PubMed Abstract: 
  

  Recently the definition of the metazoan RNA polymerase II and archaeal core promoters has been expanded to include a region immediately upstream of the TATA box called the B recognition element (BRE), so named because eukaryal transcription factor TFIIB and its archaeal orthologue TFB interact with the element in a sequence-specific manner. Here we present the 2.4-A crystal structure of archaeal TBP and the C-terminal core of TFB (TFB(c)) in a complex with an extended TATA-box-containing promoter that provides a detailed picture of the stereospecific interactions between the BRE and a helix-turn-helix motif in the C-terminal cyclin repeat of TFB(c). This interaction is important in determining the level of basal transcription and explicitly defines the direction of transcription.

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Organizational Affiliation: 

Department of Molecular Biophysics, Yale University, New Haven CT 06511, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 57.31 kDa 
• Atom Count: 4,147 
• Modelled Residue Count: 429 
• Deposited Residue Count: 429 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
TATA-BINDING PROTEIN	C [auth A]	181	Pyrococcus woesei	Mutation(s): 0
UniProt
Find proteins for P62001 (Pyrococcus woesei) Explore P62001  Go to UniProtKB:  P62001

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
TRANSCRIPTION INITIATION FACTOR IIB	D [auth B]	201	Pyrococcus woesei	Mutation(s): 1
UniProt
Find proteins for P61999 (Pyrococcus woesei) Explore P61999  Go to UniProtKB:  P61999

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA 24-MER: BRE+TATA-BOX	A [auth C]	24	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA 23-MER: BRE+TATA-BOX	B [auth D]	23	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.245 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: I 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 174.2	α = 90
b = 174.2	β = 90
c = 174.2	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALA	data scaling
CNS	refinement
HKL-2000	data reduction
CCP4	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-11-15 
Deposition Author(s): Littlefield, O., Korkhin, Y., Sigler, P.B.

Revision History  

• Version 1.0: 1999-11-15
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-11-03
  Changes: Database references
• Version 1.4: 2024-10-30
  Changes: Data collection, Structure summary