3S2D

RNA Polymerase II Initiation Complex with a 5-nt RNA containing a 5Br-U

Summary for 3S2D

• Entry DOI: 10.2210/pdb3s2d/pdb
• Related: 3S1R
• Descriptor: DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerases I, II, and III subunit RPABC4, RNA (5'-R(*AP*GP*GP*(5BU)P*G)-3'), ... (14 entities in total)
• Functional Keywords: rna polymerase ii, initiation complex, transcription-rna-dna complex, transcription/rna/dna
• Biological source: Saccharomyces cerevisiae S288c (Baker's yeast); More
• Cellular location: Nucleus: P04050 P08518 P16370 P20434 P20436 P38902; Nucleus, nucleolus : P40422 P27999 P22139; Cytoplasm : P20435
• Total number of polymer chains: 12
• Total formula weight: 480751.22

Authors

Liu, X.,Bushnell, D.A.,Silva, D.A.,Huang, X.,Kornberg, R.D. (deposition date: 2011-05-16, release date: 2011-08-10, Last modification date: 2023-09-13)

Primary citation

Liu, X.,Bushnell, D.A.,Silva, D.A.,Huang, X.,Kornberg, R.D.
Initiation complex structure and promoter proofreading.
Science, 333:633-637, 2011

PubMed 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.

PubMed: 21798951
DOI: 10.1126/science.1206629

Experimental method

X-RAY DIFFRACTION (3.2 Å)