3GTL: Backtracked RNA Polymerase II Complex With 13mer With G<>u Mismatch

Citation:
Abstract
Transcribing RNA polymerases oscillate between three stable states, two of which, pre- and posttranslocated, were previously subjected to x-ray crystal structure determination. We report here the crystal structure of RNA polymerase II in the third state, the reverse translocated, or "backtracked" state. The defining feature of the backtracked structure is a binding site for the first backtracked nucleotide. This binding site is occupied in case of nucleotide misincorporation in the RNA or damage to the DNA, and is termed the "P" site because it supports proofreading. The predominant mechanism of proofreading is the excision of a dinucleotide in the presence of the elongation factor SII (TFIIS). Structure determination of a cocrystal with TFIIS reveals a rearrangement whereby cleavage of the RNA may take place.
PDB ID: 3GTLDownload
MMDB ID: 73188
PDB Deposition Date: 2009/3/27
Updated in MMDB: 2012/10 
Experimental Method:
x-ray diffraction
Resolution: 3.38  Å
Source Organism:
synthetic construct
Similar Structures:
Biological Unit for 3GTL: tridecameric; determined by author and by software (PISA)
Molecular Components in 3GTL
Label Count Molecule
Proteins (10 molecules)
1
DNA-directed RNA Polymerase II Subunit Rpb1
Molecule annotation
1
DNA-directed RNA Polymerase II Subunit Rpb2
Molecule annotation
1
DNA-directed RNA Polymerase II Subunit Rpb3
Molecule annotation
1
DNA-directed RNA Polymerases I, II, and III Subunit Rpabc1
Molecule annotation
1
DNA-directed RNA Polymerases I, II, and III Subunit Rpabc2
Molecule annotation
1
DNA-directed RNA Polymerases I, II, and III Subunit Rpabc3
Molecule annotation
1
DNA-directed RNA Polymerase II Subunit Rpb9
Molecule annotation
1
DNA-directed RNA Polymerases I, II, and III Subunit Rpabc5
Molecule annotation
1
DNA-directed RNA Polymerase II Subunit Rpb11
Molecule annotation
1
DNA-directed RNA Polymerases I, II, and III Subunit Rpabc4
Molecule annotation
Nucleotides(3 molecules)
1
RNA (5'-r(*ap*up*cp*gp*ap*gp*ap*gp*gp*ap*up*up*c)-3')
Molecule annotation
1
DNA (28-mer)
Molecule annotation
1
DNA (5'-d(*cp*tp*gp*cp*tp*tp*ap*tp*cp*gp*gp*tp*ap*g)-3')
Molecule annotation
Chemicals (9 molecules)
1
8
2
1
* Click molecule labels to explore molecular sequence information.

Citing MMDB
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