2B63

Complete RNA Polymerase II-RNA inhibitor complex

Summary for 2B63

• Entry DOI: 10.2210/pdb2b63/pdb
• Descriptor: 31-MER, DNA-directed RNA polymerase II subunit 9, DNA-directed RNA polymerases I/II/III subunit 10, ... (15 entities in total)
• Functional Keywords: rna polymerase ii, rna, aptamer, protein-rna complex, inhibitor, transferase-rna complex, transferase/rna
• Biological source: Saccharomyces cerevisiae (baker's yeast); More
• Cellular location: Nucleus: P04050 P38902 P08518 P16370 P20433 P20434 P34087 P20436 P27999; Nucleus, nucleolus: P22139 P40422; Cytoplasm: P20435
• Total number of polymer chains: 13
• Total formula weight: 525029.34

Authors

Kettenberger, H.,Eisenfuehr, A.,Brueckner, F.,Theis, M.,Famulok, M.,Cramer, P. (deposition date: 2005-09-30, release date: 2005-12-06, Last modification date: 2023-08-23)

Primary citation

Kettenberger, H.,Eisenfuehr, A.,Brueckner, F.,Theis, M.,Famulok, M.,Cramer, P.
Structure of an RNA polymerase II-RNA inhibitor complex elucidates transcription regulation by noncoding RNAs
Nat.Struct.Mol.Biol., 13:44-48, 2006

PubMed Abstract: The noncoding RNA B2 and the RNA aptamer FC bind RNA polymerase (Pol) II and inhibit messenger RNA transcription initiation, but not elongation. We report the crystal structure of FC(*), the central part of FC RNA, bound to Pol II. FC(*) RNA forms a double stem-loop structure in the Pol II active center cleft. B2 RNA may bind similarly, as it competes with FC(*) RNA for Pol II interaction. Both RNA inhibitors apparently prevent the downstream DNA duplex and the template single strand from entering the cleft after DNA melting and thus interfere with open-complex formation. Elongation is not inhibited, as nucleic acids prebound in the cleft would exclude the RNA inhibitors. The structure also indicates that A-form RNA could interact with Pol II similarly to a B-form DNA promoter, as suggested for the bacterial transcription inhibitor 6S RNA.

PubMed: 16341226
DOI: 10.1038/nsmb1032

Experimental method

X-RAY DIFFRACTION (3.8 Å)