1D3U

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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.USA 96: 13668-13673


  • 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 TF ...

    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.


    Related Citations: 
    • New core promoter element in RNA polymerase II-dependent transcription: sequence-specific DNA binding by transcription factor IIB
      Lagrange, T.,Kapanidis, A.N.,Tang, H.,Reinberg, D.,Ebright, R.H.
      (1998) Genes Dev. 12: 34
    • The 2.1-angstrom crystal structure of an archaeal preinitiation complex: TATA- box-binding protein/transcription factor (II)B core/TATA-box
      Kosa, P.F.,Ghosh, G.,DeDecker, B.S.,Sigler, P.B.
      (1997) Proc.Natl.Acad.Sci.USA 94: 6042
    • Sequence-specific DNA binding by the S. shibatae TFIIB homolog, TFB, and its effect on promoter strength
      Qureshi, S.A.,Jackson, S.P.
      (1998) Mol.Cell 1: 389
    • The orientation of the transcription preinitiation complex in Archaea
      Bell, S.D.,Kosa, P.L.,Sigler, P.B.,Jackson, S.P.
      (1999) Proc.Natl.Acad.Sci.USA 96: --


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
TATA-BINDING PROTEIN
A
181Pyrococcus woeseiMutation(s): 0 
Gene Names: tbp
Find proteins for P62001 (Pyrococcus woesei)
Go to UniProtKB:  P62001
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
TRANSCRIPTION INITIATION FACTOR IIB
B
201Pyrococcus woeseiMutation(s): 1 
Gene Names: tfb
Find proteins for P61999 (Pyrococcus woesei)
Go to UniProtKB:  P61999
Entity ID: 1
MoleculeChainsLengthOrganism
DNA 24-MER: BRE+TATA-BOXC24N/A
Entity ID: 2
MoleculeChainsLengthOrganism
DNA 23-MER: BRE+TATA-BOXD23N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.206 
  • Space Group: I 21 3
Unit Cell:
Length (Å)Angle (°)
a = 174.200α = 90.00
b = 174.200β = 90.00
c = 174.200γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
CCP4data scaling
CNSphasing
CNSrefinement
HKL-2000data collection
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-11-15
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance