Protein Name

RNA polymerase II-transcribing complex in the post-translocation state


Saccharomyces cerevisiae (Baker's yeast)

Biological Context

During transcription RNA polymerases catalyze the synthesis of the RNA strand complementary to the template DNA. RNA polymerase II (Pol II) helps with the synthesis of the mRNA precursor.

Recently, the structure of Pol II-transcribing complex has been determined. In this complex, Pol II composed of ten subunits associates with the RNA-DNA hybrid helix. From this structure analysis, the two critical events, the selection of a ribonucleotide triphosphate complementary to the template DNA and the separation of the RNA-DNA hybrid, have been revealed. This information had not been obtainable from previous structural studies. Because the prior step of generating the transcription complex involves the use of duplex DNA with a single-stranded “tail” protruding from the 3’ end, the enzyme fails to separate the transcript from the template and to add a ribonucleotide triphosphate at the growing end.

Structure Description


On the other hand, the RNA-DNA hybrid helix in this complex has a vacancy for the next ribonucleotide triphosphate at the growing end. Therefore a misincorporation will not occur. The structural features of three protein loops, “lib”, ”rudder” and “fork loop 1”, which play a key role in the separation of the RNA-DNA hybrid, have been revealed for the first time. The lib serves as a wedge to separate the hybrid, the rudder prevents the DNA from re-associating with the RNA, and the fork loop 1 decides the range of the hybrid separation. Thus, in the Pol II-hybrid complex a strand/loop network is formed that leads to the separation of the RNA from the template DNA at position –8.

The separated RNA strand exits the Pol II active-center region through an “exit pore” near the three loops, but the DNA strand exits above the pore, preventing any reassociation. Due to the newly made observations described above, this analysis has provided new insights into transcription.

Protein Data Bank (PDB)



  • Westover, K.D. Bushnell, D.A. Kornberg, R.D.; "Structural Basis of Transcription: Separation of RNA from DNA by RNA Polymerase II"; Science; (2004) 303:1014-1016 PubMed:14963331.


author: Yuko Tsuchiya

Japanese version:PDB:1SFO