3H3V: Yeast RNAP II containing poly(A)-signal sequence in the active site

Citation:
Abstract
Termination of RNA polymerase (pol) II transcription in vivo requires the 5'-RNA exonuclease Rat1. It was proposed that Rat1 degrades RNA from the 5'-end that is created by transcript cleavage, catches up with elongating pol II, and acts like a Torpedo that removes pol II from DNA. Here we test the Torpedo model in an in vitro system based on bead-coupled pol II elongation complexes (ECs). Recombinant Rat1 complexes with Rai1, and with Rai1 and Rtt103, degrade RNA extending from the EC until they reach the polymerase surface but fail to terminate pol II. Instead, the EC retains an approximately 18-nucleotide RNA that remains with its 3'-end at the active site and can be elongated. Thus, pol II termination apparently requires a factor or several factors in addition to Rat1, Rai1, and Rtt103, post-translational modifications of these factors, or unusual reaction conditions.
PDB ID: 3H3VDownload
MMDB ID: 73367
PDB Deposition Date: 2009/4/17
Updated in MMDB: 2017/11
Experimental Method:
x-ray diffraction
Resolution: 4  Å
Source Organism:
Saccharomyces cerevisiae
Similar Structures:
Biological Unit for 3H3V: pentadecameric; determined by author
Molecular Components in 3H3V
Label Count Molecule
Proteins (12 molecules)
1
DNA-directed RNA Polymerase II Subunit Rpb1(Gene symbol: RPO21)
Molecule annotation
1
DNA-directed RNA Polymerase II Subunit Rpb2(Gene symbol: RPB2)
Molecule annotation
1
DNA-directed RNA Polymerase II Subunit Rpb3(Gene symbol: RPB3)
Molecule annotation
1
DNA-directed RNA Polymerase II Subunit Rpb4(Gene symbol: RPB4)
Molecule annotation
1
DNA-directed RNA Polymerases I, II, and III Subunit Rpabc1(Gene symbol: RPB5)
Molecule annotation
1
DNA-directed RNA Polymerases I, II, and III Subunit Rpabc2(Gene symbol: RPO26)
Molecule annotation
1
DNA-directed RNA Polymerase II Subunit Rpb7(Gene symbol: RPB7)
Molecule annotation
1
DNA-directed RNA Polymerases I, II, and III Subunit Rpabc3(Gene symbol: RPB8)
Molecule annotation
1
DNA-directed RNA Polymerase II Subunit Rpb9(Gene symbol: RPB9)
Molecule annotation
1
DNA-directed RNA Polymerases I, II, and III Subunit Rpabc5(Gene symbol: RPB10)
Molecule annotation
1
DNA-directed RNA Polymerase II Subunit Rpb11(Gene symbol: RPB11)
Molecule annotation
1
DNA-directed RNA Polymerases I, II, and III Subunit Rpabc4(Gene symbol: RPC10)
Molecule annotation
Nucleotides(3 molecules)
1
5'-d(*ap*gp*cp*tp*cp*ap*ap*gp*tp*ap*gp*cp*tp*gp*cp*tp*tp*tp*ap*tp*tp*gp*cp*ap*tp*t)-3'
Molecule annotation
1
5'-d(*cp*ap*gp*cp*tp*ap*cp*tp*tp*gp*ap*gp*cp*t)-3'
Molecule annotation
1
5'-r(*up*gp*cp*ap*up*up*up*cp*gp*cp*ap*ap*up*ap*ap*a)-3'
Molecule annotation
Chemicals (9 molecules)
1
8
2
1
* Click molecule labels to explore molecular sequence information.

Citing MMDB
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