1Y77

Complete RNA Polymerase II elongation complex with substrate analogue GMPCPP

Summary for 1Y77

• Entry DOI: 10.2210/pdb1y77/pdb
• Related: 1Y1W
• Descriptor: 5'-D(P*AP*GP*TP*AP*CP*TP*TP*AP*CP*T*CP*GP*CP*CP*TP*GP*GP*TP*CP*TP*G)-3', DNA-directed RNA polymerase II 19 kDa polypeptide, DNA-directed RNA polymerases I, II, and III 14.5 kDa polypeptide, ... (18 entities in total)
• Functional Keywords: transcription, substrate, ntp, elongation, transferase-dna-rna hybrid complex, transferase/dna-rna hybrid
• 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: 15
• Total formula weight: 526383.23

Authors

Kettenberger, H.,Armache, K.-J.,Cramer, P. (deposition date: 2004-12-08, release date: 2005-01-04, Last modification date: 2024-10-30)

Primary citation

Kettenberger, H.,Armache, K.-J.,Cramer, P.
Complete RNA Polymerase II Elongation Complex Structure and Its Interactions with NTP and TFIIS
Mol.Cell, 16:955-965, 2004

PubMed Abstract: The crystal structure of the complete 12 subunit RNA polymerase (pol) II bound to a transcription bubble and product RNA reveals incoming template and nontemplate DNA, a seven base pair DNA/RNA hybrid, and three nucleotides each of separating DNA and RNA. The complex adopts the posttranslocation state and accommodates a cocrystallized nucleoside triphosphate (NTP) substrate. The NTP binds in the active site pore at a position to interact with a DNA template base. Residues surrounding the NTP are conserved in all cellular RNA polymerases, suggesting a universal mechanism of NTP selection and incorporation. DNA-DNA and DNA-RNA strand separation may be explained by pol II-induced duplex distortions. Four protein loops partition the active center cleft, contribute to embedding the hybrid, prevent strand reassociation, and create an RNA exit tunnel. Binding of the elongation factor TFIIS realigns RNA in the active center, possibly converting the elongation complex to an alternative state less prone to stalling.

PubMed: 15610738
DOI: 10.1016/j.molcel.2004.11.040

Experimental method

X-RAY DIFFRACTION (4.5 Å)