Primary Citation PubMed: 15610738
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Nano positioning system reveals the course of upstream and nontemplate DNA within the RNA polymerase II elongation complex.
(2009) Nucleic Acids Res 37
PubMed: 19620213 | PubMedCentral: PMC2761271 | DOI: 10.1093/nar/gkp601
This represents the single-stranded region of the nontemplate strand and the upstream duplex DNA, neither of which are visible in the crystal structure of the Pol II EC 1Y1W ( 6 ).
Publication Year: 2009
Molecular mechanisms of RNA polymerase--the F/E (RPB4/7) complex is required for high processivity in vitro.
(2010) Nucleic Acids Res 38
PubMed: 19906731 | PubMedCentral: PMC2811020 | DOI: 10.1093/nar/gkp928
‘The S. shibatae RNAP structure (pdb 2WAQ) was manually superimposed on the DNA–RNA scaffold of the S. cerevisiae RNAPII elongation complex (DNA in yellow, RNA in red, pdb 1Y1W).
Publication Year: 2010
Mechanism of chromatin remodeling and recovery during passage of RNA polymerase II.
(2009) Nat Struct Mol Biol 16
PubMed: 19935686 | PubMedCentral: PMC2919570 | DOI: 10.1038/nsmb.1689
To evaluate the possibility of Ø-loop formation by Pol II, we modeled the Ø-loop by docking the high-resolution structures of yeast Pol II EC onto the nucleosome (PDB IDs 1aoi and 1y1w... see refs.
The structures of a nucleosome and yeast Pol II EC (PDB IDs 1aoi and 1y1w, see refs.
Molecular architecture of the human Mediator-RNA polymerase II-TFIIF assembly.
(2011) PLoS Biol 9
PubMed: 21468301 | PubMedCentral: PMC3066130 | DOI: 10.1371/journal.pbio.1000603
Docking was also completed using each of the complete 12-subunit pol II structures found in the RCSB Protein Data Bank (1NT9, 1PQV, 1WCM, 1Y1W, 1Y1Y, 1Y77, 2B8K, 2B63, 2JA5, 2JA6, 2JA7, 2JA8, 2VUM, 3F... I, 3HOU, 3HOV, 3HOW, 3HOX, 3HOY, 3HOZ, 3K1F), with identical results.
Publication Year: 2011
Structural basis of initial RNA polymerase II transcription.
(2011) EMBO J 30
PubMed: 22056778 | PubMedCentral: PMC3243610 | DOI: 10.1038/emboj.2011.396
( B ) Comparison of DNA–RNA hybrids in the 4-nt RNA structure and EC structure (light green, PDB 1Y1W) reveals a tilted hybrid conformation.
The downstream DNA is in the standard position of the EC (PDB code 1Y1W) ( Kettenberger et al, 2004 ) (6 nt) or in an alternative position previously observed for a DNA lesion-containing complex (PDB code 2JA6) ( Brueckner et al, 2007 ) (4 nt), or as a mixture of these two states (5 nt).
Composite structural motifs of binding sites for delineating biological functions of proteins.
(2012) PLoS One 7
PubMed: 22347478 | PubMedCentral: PMC3275580 | DOI: 10.1371/journal.pone.0031437
Similarly, there are PDB entries of yeast RNA polymerase II with or without bound DNA/RNA in which the subunit RPB2 (e.g., PDB 1I3Q  , chain B and 1Y1W  , chain B) share some elementary motifs... for protein binding, but other corresponding protein binding sites belong to different elementary motifs due to slight conformational changes (not shown), and an elementary motif for binding DNA is present in only one of the entries; thus these subunits identical in amino acid sequence have different composite motifs which are connected by edges of the common protein binding motifs and of the common sequence.
Publication Year: 2012
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
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–D... A/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.
Interestingly, FL1 is also ordered in both archaeal structures (in apo-Pol II it is disordered; PDB ID 1Y1W), probably due to being shorter by ∼6 residues compared with the equivalent FL1 in Pol II, but it adopts an ‘up’ conformation ( Figure 3 C) that may lock down once RNA is synthesized.
( 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).
As with FL1, FL2 is well-defined ( Figure 2 A) as is its eukaryal counterpart in the complete elongation complex (PDB ID 1Y1W).
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