Protein Name

Transcription factor IIB / RNA polymerase II complex


Saccharomyces cerevisiae (Baker's yeast)

Biological Context

In eukaryotes, many proteins are involved in transcription initiation and form transient large complexes. RNA polymerase II (pol II) assembles five general transcription factors (TFIIB, TFIID, TFIIE, TFIIF, TFIIH) and a mediator at the promoter DNA before the initiation of transcription. The transient complex recognizes the promoter DNA and regulates transcription. It is known that TFIIB and TFIID, in particular, are essential for the recognition of the promoter DNA.

Structure Description


The structure of the complex of the 10-subunit pol II from budding yeast with TFIIB has been determined. This structure analysis revealed the following features. The N-terminal zinc ribbon domain of TFIIB binds to the dock domain of pol II and the C-terminal domain binds directly to the upstream and downstream regions of the promoter region, TATA box. The finger domain on the C-terminal side of the N-terminal zinc ribbon domain is inserted into the polymerase active center of pol II. As a result, TFIIB acts as a bridge between the promoter DNA and pol II, and marks the start site of transcription. Transcription is then initiated, unwinding the DNA. Together with the structures of other transcription factors and the pol II - RNA-DNA hybrid complex determined previously along with the pol II-TFIIB complex, key features of the mechanism of transcription initiation have been identified. The TATA box binding protein (TBP) subunit of TFIID recognizes the promoter TATA box, and bends the DNA. As a consequence, the C-terminal domain of TFIIB (TFIIBc) can easily bind to the DNA. TFIIB determines the start site of transcription at two levels; one is a coarse setting by TFIIBc binding to the TATA box and another is a fine one by the finger domain of the N-terminal domain of TFIIB (TFIIBn) interacting with the template DNA single strand at the pol II active center. The fine setting involves interaction with the initiator region of some promoters by the TFIIBn finger domain. Such interactions of the TFIIBn finger domain may stabilize the initiation complex containing the RNA-DNA hybrid regions. Furthermore, the conformational change caused by the pol II-TFIIB interaction causes TFIIE to bind to a jaw-shaped lobe of pol II. Due to these interactions, the promoter DNA passes straight over TFIIE, TFIIF and TFIIH of the initiation complex and wraps them. Thus, until double-strand DNA is unwound, pol II does not interact further with DNA.

Protein Data Bank (PDB)



Bushnell, D.A. Westover, K.D. Davis, R. Kornberg, R.D.; "Structural basis of transcription: an RNA polymerase II-TFIIB cocrystal at 4.5 angstroms"; Science; (2004) 303:983-988. PubMed:14963322


UniProt:P04050 UniProt:P08518 UniProt:P16370 UniProt:P20434 UniProt:P20435 UniProt:P20436 UniProt:P27999 UniProt:P22139 UniProt:P38902 UniProt:P40422

author: Yuko Tsuchiya

Japanese version:PDB:1R5U