1C9B

CRYSTAL STRUCTURE OF A HUMAN TBP CORE DOMAIN-HUMAN TFIIB CORE DOMAIN COMPLEX BOUND TO AN EXTENDED, MODIFIED ADENOVIRAL MAJOR LATE PROMOTER (ADMLP)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis of preinitiation complex assembly on human pol II promoters.

Tsai, F.T.Sigler, P.B.

(2000) EMBO J 19: 25-36

  • DOI: 10.1093/emboj/19.1.25
  • Primary Citation of Related Structures:  
    1C9B

  • PubMed Abstract: 
  • Transcription initiation requires the assembly of a preinitiation complex (PIC), which is nucleated through binding of the TATA-box binding protein (TBP) to the promoter. Biochemical studies have shown, however, that TBP recognizes the TATA-box in bo ...

    Transcription initiation requires the assembly of a preinitiation complex (PIC), which is nucleated through binding of the TATA-box binding protein (TBP) to the promoter. Biochemical studies have shown, however, that TBP recognizes the TATA-box in both orientations and, therefore, cannot account for the directionality of PIC assembly. Transcription factor IIB (TFIIB) is essential for transcription initiation from RNA polymerase II promoters. Recent functional studies have identified a specific 7 bp TFIIB recognition element (BRE) immediately upstream of the TATA-box. We present here the 2.65 A resolution crystal structure of a human TFIIBc-TBPc complex bound to an idealized and extended adenovirus major late promoter. This structure now reveals that human TFIIBc binds to the promoter asymmetrically through base-specific contacts in the major groove upstream and in the minor groove downstream of the TATA-box. Binding of TFIIBc is, therefore, synergistic with TBPc requiring the distortion of the TATA-box. Thus, the newly described TFIIBc-DNA interface is likely to be a key determinant for the unidirectional assembly of a functional PIC.


    Related Citations: 
    • 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
    • Polarity of transcription on Pol II and archaeal promoters: where is the "one- way sign" and how is it read?
      Tsai, F.T.F., Littlefield, O., Kosa, P.F., Cox, J.M., Schepartz, A., Sigler, P.B.
      (1998) Cold Spring Harb Symp Quant Biol 63: 53
    • Crystal structure of a TFIIB-TBP-TATA-element ternary complex
      Nikolov, D.B., Chen, H., Halay, E.D., Usheva, A.A., Hisatake, K., Lee, D.K., Roeder, R.G., Burley, S.K.
      (1995) Nature 377: 119
    • The 2.1-A 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., Sigler, P.B.
      (1997) Proc Natl Acad Sci U S A 94: 6042
    • Solution structure of the C-terminal core domain of human TFIIB: similarity to cyclin A and interaction with TATA-binding protein
      Bagby, S., Kim, S., Maldonado, E., Tong, K.I., Reinberg, D., Ikura, M.
      (1995) Cell 82: 857

    Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry and the Howard Hughes Medical Institute, Yale University, New Haven, CT 06511, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
GENERAL TRANSCRIPTION FACTOR IIBAEIMQ207Homo sapiensMutation(s): 0 
Gene Names: GTF2BTF2BTFIIB
EC: 2.3.1.48
Find proteins for Q00403 (Homo sapiens)
Explore Q00403 
Go to UniProtKB:  Q00403
NIH Common Fund Data Resources
PHAROS  Q00403
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
TATA BOX BINDING PROTEINBFJNR180Homo sapiensMutation(s): 0 
Gene Names: TBPGTF2D1TF2DTFIID
Find proteins for P20226 (Homo sapiens)
Explore P20226 
Go to UniProtKB:  P20226
NIH Common Fund Data Resources
PHAROS  P20226
Protein Feature View
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  • Reference Sequence
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  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    ADMLP TATA-BOX DNA CONTAINING IIB RECOGNITION ELEMENTD, H, L, P, T18N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 1
      MoleculeChainsLengthOrganismImage
      ADMLP TATA-BOX DNA CONTAINING IIB RECOGNITION ELEMENTC, G, K, O, S18N/A
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.65 Å
      • R-Value Free: 0.260 
      • R-Value Work: 0.229 
      • R-Value Observed: 0.231 
      • Space Group: P 1 21 1
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 118.45α = 90
      b = 122.298β = 113.08
      c = 140.217γ = 90
      Software Package:
      Software NamePurpose
      AMoREphasing
      CNSrefinement
      DENZOdata reduction
      SCALEPACKdata scaling

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History 

      • Version 1.0: 2000-01-10
        Type: Initial release
      • Version 1.1: 2008-04-27
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Version format compliance