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 

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

  • 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.USA 96: 13668
    • 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.USA 94: 6042
    • 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
    • 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 Harbor Symp.Quant.Biol. 63: 53
    • 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: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
GENERAL TRANSCRIPTION FACTOR IIB
A, E, I, M, Q
207Homo sapiensMutation(s): 0 
Gene Names: GTF2B (TF2B, TFIIB)
EC: 2.3.1.48
Find proteins for Q00403 (Homo sapiens)
Go to Gene View: GTF2B
Go to UniProtKB:  Q00403
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
TATA BOX BINDING PROTEIN
B, F, J, N, R
180Homo sapiensMutation(s): 0 
Gene Names: TBP (GTF2D1, TF2D, TFIID)
Find proteins for P20226 (Homo sapiens)
Go to Gene View: TBP
Go to UniProtKB:  P20226
Entity ID: 1
MoleculeChainsLengthOrganism
ADMLP TATA-BOX DNA CONTAINING IIB RECOGNITION ELEMENTC,G,K,O,S18N/A
Entity ID: 2
MoleculeChainsLengthOrganism
ADMLP TATA-BOX DNA CONTAINING IIB RECOGNITION ELEMENTD,H,L,P,T18N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.229 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 118.450α = 90.00
b = 122.298β = 113.08
c = 140.217γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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