3RZD: RNA Polymerase II Initiation Complex With a 5-nt RNA

Citation:
Abstract
The initiation of transcription by RNA polymerase II is a multistage process. X-ray crystal structures of transcription complexes containing short RNAs reveal three structural states: one with 2- and 3-nucleotide RNAs, in which only the 3'-end of the RNA is detectable; a second state with 4- and 5-nucleotide RNAs, with an RNA-DNA hybrid in a grossly distorted conformation; and a third state with RNAs of 6 nucleotides and longer, essentially the same as a stable elongating complex. The transition from the first to the second state correlates with a markedly reduced frequency of abortive initiation. The transition from the second to the third state correlates with partial "bubble collapse" and promoter escape. Polymerase structure is permissive for abortive initiation, thereby setting a lower limit on polymerase-promoter complex lifetime and allowing the dissociation of nonspecific complexes. Abortive initiation may be viewed as promoter proofreading, and the structural transitions as checkpoints for promoter control.
PDB ID: 3RZDDownload
MMDB ID: 92583
PDB Deposition Date: 2011/5/11
Updated in MMDB: 2011/08 
Experimental Method:
x-ray diffraction
Resolution: 3.3  Å
Source Organism:
Saccharomyces cerevisiae S288C
Similar Structures:
Biological Unit for 3RZD: dodecameric; determined by author and by software (PISA)
Molecular Components in 3RZD
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(2 molecules)
1
RNA (5'-r(*ap*gp*ap*gp*g)-3')
Molecule annotation
1
DNA (5'- D(*cp*tp*ap*cp*cp*gp*ap*tp*ap*ap*gp*cp*ap*gp*ap*cp*gp*ap*tp*cp*cp*tp* Cp*tp*cp*gp*ap*tp*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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