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: https://doi.org/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 both orientations and, therefore, cannot account for the directionality of PIC assembly ...

    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

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
GENERAL TRANSCRIPTION FACTOR IIBK [auth A],
M [auth E],
O [auth I],
Q [auth M],
S [auth Q]		207Homo sapiensMutation(s): 0 
Gene Names: GTF2B, TF2B, TFIIB
EC: 2.3.1.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q00403 (Homo sapiens)
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Go to UniProtKB:  Q00403
PHAROS:  Q00403
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UniProt GroupQ00403
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
TATA BOX BINDING PROTEINL [auth B],
N [auth F],
P [auth J],
R [auth N],
T [auth R]		180Homo sapiensMutation(s): 0 
Gene Names: TBP, GTF2D1, TF2D, TFIID
UniProt & NIH Common Fund Data Resources
Find proteins for P20226 (Homo sapiens)
Explore P20226 
Go to UniProtKB:  P20226
PHAROS:  P20226
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UniProt GroupP20226
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Entity ID: 1
MoleculeChainsLengthOrganismImage
ADMLP TATA-BOX DNA CONTAINING IIB RECOGNITION ELEMENTA [auth C],
C [auth G],
E [auth K],
G [auth O],
I [auth S]		18N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
ADMLP TATA-BOX DNA CONTAINING IIB RECOGNITION ELEMENTB [auth D],
D [auth H],
F [auth L],
H [auth P],
J [auth T]		18N/A
Protein Feature View
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  • Reference Sequence
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

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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