4XLP: Crystal Structure Of T.aquaticus Transcription Initiation Complex Containing Upstream Fork Promoter

Citation:
Abstract
Initiation of transcription is a primary means for controlling gene expression. In bacteria, the RNA polymerase (RNAP) holoenzyme binds and unwinds promoter DNA, forming the transcription bubble of the open promoter complex (RPo). We have determined crystal structures, refined to 4.14 A-resolution, of RPo containing Thermus aquaticus RNAP holoenzyme and promoter DNA that includes the full transcription bubble. The structures, combined with biochemical analyses, reveal key features supporting the formation and maintenance of the double-strand/single-strand DNA junction at the upstream edge of the -10 element where bubble formation initiates. The results also reveal RNAP interactions with duplex DNA just upstream of the -10 element and potential protein/DNA interactions that direct the DNA template strand into the RNAP active site. Addition of an RNA primer to yield a 4 base-pair post-translocated RNA:DNA hybrid mimics an initially transcribing complex at the point where steric clash initiates abortive initiation and sigma(A) dissociation.
PDB ID: 4XLPDownload
MMDB ID: 132818
PDB Deposition Date: 2015/1/13
Updated in MMDB: 2017/10
Experimental Method:
x-ray diffraction
Resolution: 4  Å
Source Organism:
synthetic construct
Similar Structures:
Biological Unit for 4XLP: octameric; determined by author
Molecular Components in 4XLP
Label Count Molecule
Proteins (6 molecules)
2
DNA-directed RNA Polymerase Subunit Alpha
Molecule annotation
1
DNA-directed RNA Polymerase Subunit Beta
Molecule annotation
1
DNA-directed RNA Polymerase Subunit Beta'
Molecule annotation
1
DNA-directed RNA Polymerase Subunit Omega
Molecule annotation
1
RNA Polymerase Sigma Factor Siga
Molecule annotation
Nucleotides(2 molecules)
1
DNA (30-mer)
Molecule annotation
1
DNA (25-mer)
Molecule annotation
Chemicals (3 molecules)
1
2
2
1
* Click molecule labels to explore molecular sequence information.

Citing MMDB
.