Primary Citation PubMed: 22056778
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Structural basis of initial RNA polymerase II transcription.
(2011) EMBO J 30
PubMed: 22056778 | PubMedCentral: PMC3243610 | DOI: 10.1038/emboj.2011.396
Table 1 Pol II–nucleic acid complex structures elucidating initial transcription Complex Tailed-template DNA a RNA (−1 and upstream) NTP (+1) Resolution (Å) R free (... 0025;) Hybrid conformation b Trigger loop c PDB code 1 DNA-1 — — 3.8 19.1 – (Open complex) Open 4A3I 2 DNA-1 2 nt — 3.5 20.2 Standard Open 4A3G 3 DNA-2 2 nt GMPCPP 3.7 19.6 Standard Closed 4A3J 4 4 nt — 3.5 20.1 Tilted Open 4A3B 5 4 nt AMPCPP 3.9 20.7 Standard Closed 4A3M 6 5 nt — 3.5 20.1 Tilted Open 4A3C 7 5 nt AMPCPP 3.4 20.6 Standard Closed 4A3E 8 6 nt — 3.4 18.7 Tilted Open 4A3D 9 6 nt AMPCPP 3.5 20.7 Standard Closed 4A3F 10 7 nt — 3.5 19.0 Tilted Open 4A3K 11 7 nt AMPCPP 3.5 21.1 Standard Closed 4A3L a Sequences for nucleic acids are in Figure 1B .
Publication Year: 2011
Structural and functional analyses of the interaction of archaeal RNA polymerase with DNA.
(2012) Nucleic Acids Res 40
PubMed: 22848102 | PubMedCentral: PMC3479171 | DOI: 10.1093/nar/gks692
Finally, residues from 87 to 99 within the trigger loop (Rpo1C: amino acids 71–116) remain disordered as it is also the case of the eukaryal Pol II OC (PDB ID 4A3I) and transcription elongatio... complex (TEC) (PDB ID 1R9T).
( A ) Stereo-figure of the DNA with 2Fo–Fc map (slate-blue mesh at 1.0σ) with refined DNA phases included; a RNAP’s subunits as cartoon tube with semi-transparent surface and DNA coloured as Figure 1 ; in light pink and steel blue the DNA backbone (as tube) of the eukaryotic Pol II–DNA open complex (PDB ID 4A3I) and of Pol II DNA/RNA elongation complex (PDB ID 1R9T) superimposed onto the DNA bound to our a RNAP [corresponding superimpositions of Rpb1 onto Rpo1, RMSD 2.8 Å, 1183 Cαs equivalences and 2.8Å, 1174 Cαs equivalences were performed using the Structural Homology Program (SHP) ( 33 )]; dark blue, light pink, and steel blue straight lines correspond to helix axes; black curved arrow indicates the tilting required (∼17°) for superimposing the DNA of Pol II TEC (steel blue axis) onto the DNA bound to a RNAP (dark blue axis); a tilting of ∼11° in the same direction is required to superimpose the DNA of Pol II OC (light pink axis) onto the DNA bound to a RNAP (dark blue axis).
Third, contrary to the disorder/order transition observed in some important structural elements [e.g. Fork loops 1 (FL1) and 2 (FL2)] between eukaryotic naked Pol II (PDB ID 1WCM) and Pol II–DNA/RNA complexes upon nucleic acids binding (for comparison see PDB IDs 4A3I, 1R9T and 1Y1W), the archaeal apo- and DNA-bound RNAP forms do not show any striking order conversions or major re-adjustments upon DNA binding.
( A ) Left, superimposition of the eukaryotic Rpb1 (light pink cartoon tube; PDB ID 4A3I) onto the archaeal Rpo1N and Rpo1C (white smoke as cartoon tube) complexed with DNA (this study) represented as spheres (non-template and template strands in green and blue, respectively) viewed quasi along the DNA axis; analysis of the hinge movement (∼20°) that the eukaryotic Jaw domain (amino acids 1141–1275) would need to superimpose onto the archaeal counterpart was performed with SHP (Similar results were obtained using the eukaryotic Rpb1 in PDB IDs 1Y1W and 1R9T).
However, this same loop is not ordered in the Pol II open and transcribing complexes (PDB IDs 4A3I, 1R9T).
Publication Year: 2012
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