1D3U

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.212 

wwPDB Validation   3D Report Full Report


This is version 1.3 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 U S A 96: 13668-13673

  • 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 ...

    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: 
    • 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 U S A 96: --
    • 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 U S A 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
    • 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
    Organizational Affiliation: 

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



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
TATA-BINDING PROTEINC [auth A]181Pyrococcus woeseiMutation(s): 0 
Gene Names: tbp
UniProt
Find proteins for P62001 (Pyrococcus woesei)
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Go to UniProtKB:  P62001
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UniProt GroupP62001
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
TRANSCRIPTION INITIATION FACTOR IIBD [auth B]201Pyrococcus woeseiMutation(s): 1 
Gene Names: tfb
UniProt
Find proteins for P61999 (Pyrococcus woesei)
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Go to UniProtKB:  P61999
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UniProt GroupP61999
Protein Feature View
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA 24-MER: BRE+TATA-BOXA [auth C]24N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA 23-MER: BRE+TATA-BOXB [auth D]23N/A
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.212 
  • Space Group: I 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 174.2α = 90
b = 174.2β = 90
c = 174.2γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALAdata scaling
CNSrefinement
HKL-2000data reduction
CCP4data scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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