4A3C: RNA Polymerase II Initial Transcribing Complex With a 5NT DNA-rna Hybrid

Citation:
Abstract
During transcription initiation by RNA polymerase (Pol) II, a transient open promoter complex (OC) is converted to an initially transcribing complex (ITC) containing short RNAs, and to a stable elongation complex (EC). We report structures of a Pol II-DNA complex mimicking part of the OC, and of complexes representing minimal ITCs with 2, 4, 5, 6, and 7 nucleotide (nt) RNAs, with and without a non-hydrolyzable nucleoside triphosphate (NTP) in the insertion site +1. The partial OC structure reveals that Pol II positions the melted template strand opposite the active site. The ITC-mimicking structures show that two invariant lysine residues anchor the 3'-proximal phosphate of short RNAs. Short DNA-RNA hybrids adopt a tilted conformation that excludes the +1 template nt from the active site. NTP binding induces complete DNA translocation and the standard hybrid conformation. Conserved NTP contacts indicate a universal mechanism of NTP selection. The essential residue Q1078 in the closed trigger loop binds the NTP 2'-OH group, explaining how the trigger loop couples catalysis to NTP selection, suppressing dNTP binding and DNA synthesis.
PDB ID: 4A3CDownload
MMDB ID: 95131
PDB Deposition Date: 2011/9/30
Updated in MMDB: 2011/12 
Experimental Method:
x-ray diffraction
Resolution: 3.5  Å
Source Organism:
Similar Structures:
Biological Unit for 4A3C: pentadecameric; determined by author and by software (PISA)
Molecular Components in 4A3C
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 Rpabc 1(Gene symbol: RPB5)
Molecule annotation
1
DNA-directed RNA Polymerases I, II, and III Subunit Rpabc 2(Gene symbol: RPO26)
Molecule annotation
1
Rpb7, DNA-directed RNA Polymerase II Subunit Rpb7(Gene symbol: RPB7)
Molecule annotation
1
DNA-directed RNA Polymerases I, II, and III Subunit Rpabc 3(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 Rpabc 5(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 Rpabc 4(Gene symbol: RPC10)
Molecule annotation
Nucleotides(3 molecules)
1
Template DNA
Molecule annotation
1
NON Template DNA
Molecule annotation
1
Transcript RNA, 5'-r(*cp*ap*gp*gp*ap)-3'
Molecule annotation
Chemicals (9 molecules)
1
8
2
1
* Click molecule labels to explore molecular sequence information.

Citing MMDB
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