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Functional organization of the Rpb5 subunit shared by the three yeast RNA polymerases.
(2007) Nucleic Acids Res 35
PubMed: 17179178 | PubMedCentral: PMC1802627 | DOI: 10.1093/nar/gkl686
The ‘upper’ view using PDB co-ordinates 1I6H from ( 45 ) was drawn with Rasmol ( ).
Drawing based on the PDB crystallographic coordinates 1I6H (41), with Hydrogen atoms recalculated by the PDB-viewer programme.
( A ) Spatial organization of the Switch 1 loop (1378–1403), Bridge helix (C-end, positions 804–835), trigger helix (positions 1057–1089) and Rpb1-α46/47 domain (1338–1377) in RNA polymerase II, based on the PDB crystallographic coordinates 1I6H (41).
( B ) View of the same domains and of Rpb5 and Rpb9 in the elongating RNA polymerase II, based on the PDB crystallographic coordinates 1I6H ( 45 ).
Publication Year: 2007
DISPLAR: an accurate method for predicting DNA-binding sites on protein surfaces.
PubMed: 17284455 | PubMedCentral: PMC1865077 | DOI: 10.1093/nar/gkm008
Not included in this set were two nonhomologous entries (1i6h and 1w36) of protein complexes, each with more than a total of 2000 residues; these two entries were later used in an additional test of D... SPLAR.
The former 102 residues, shown in blue, cyan or green, cover 52% of the DNA-contacting residues at the substrate binding site of 1i6h with an accuracy of 66%; the latter 44 residues are shown in magenta (downstream DNA is not resolved in 1i6h).
( A ) RNA polymerase II elongation complex (PDB 1i6h).
Two of such large complexes, the RNA polymerase II elongation complex and the RecBCD–DNA complex, have their structures determined (PDB 1i6h and 1w36) ( 35 , 36 ).
A bridge to transcription by RNA polymerase.
(2008) J Biol 7
PubMed: 19090964 | PubMedCentral: PMC2776398 | DOI: 10.1186/jbiol99
BH from S. cerevisiae ( Sce ) Pol II elongation complex without substrate, PDB 1i6h (magenta) [ 11 ].
Publication Year: 2008
RNA polymerase II mutations conferring defects in poly(A) site cleavage and termination in Saccharomyces cerevisiae.
(2013) G3 (Bethesda) 3
PubMed: 23390594 | PubMedCentral: PMC3564978 | DOI: 10.1534/g3.112.004531
This figure was created from pdb file 1I6H using PyMOL (DeLano Scientific).
Publication Year: 2013
DBSI: DNA-binding site identifier.
(2013) Nucleic Acids Res 41
PubMed: 23873960 | PubMedCentral: PMC3763564 | DOI: 10.1093/nar/gkt617
Three additional APO proteins were deleted as well, as two have only CA traces (PDB IDs: 1LRP and 1BGT), and the third corresponds to 1I6H (PDB ID: 1NIK), which was deleted from our APO data set owing... to its large size.
One of the HOLO complexes (PDB ID: 1I6H) contains >2000 residues and was deleted from our test data set because predictions on this example would exert too much influence on the combined statistics for the predictive results.
RNA polymerase III-specific general transcription factor IIIC contains a heterodimer resembling TFIIF Rap30/Rap74.
PubMed: 23921640 | PubMedCentral: PMC3799434 | DOI: 10.1093/nar/gkt664
The open PIC complex was prepared by fitting the elongation complex of the Pol II structure (PDB ID: 1I6H) and the homology model of the C53/C37 dimerization domains into the Pol III EM density map (E... DB code 1802).
Computational simulation strategies for analysis of multisubunit RNA polymerases.
(2013) Chem Rev 113
PubMed: 23987500 | PubMedCentral: PMC3829680 | DOI: 10.1021/cr400046x
Table 1 Structures of RNAPs Used in Computational Simulations PDB ID resolution (Å) organism a protein nucleic acid nucleotide state TL b simulations c refs 1I6H 3.30 Sc 10 subunits T/R ... 0; pretranslocation open NMA (ENM) ( 13a ) 1I50 2.80 Sc 10 subunits open NMA (ENM) ( 13a ) 1HQM 3.30 Ta α 2 ββ′ω open NMA (ENM) ( 13a ) 1ARO 2.80 T7 T/N NMA (ENM) ( 13 ) 1CEZ 2.40 T7 NMA (ENM) ( 13 ) 1I6H 3.30 Sc 10 subunits T/N/R preinsertion open restricted MD ( 19 ) 1IW7 2.6 Tt α 2 ββ′ωσ initiation open BNM ( 15 ) 1R9T 3.5 Sc 10 subunits T/N/R ATP (E site) posttranslocation open BD ( 9 ) 1H38 2.9 T7 T/N/R preinsertion MD and umbrella sampling ( 22 ) 1S77 2.69 T7 T/N/R PP i pretranslocation MD and umbrella sampling ( 22 ) 2E2H 3.95 Sc 10 subunits T/N/R GTP posttranslocation closed MD, MSM,QM ( 7a , 16 , 17 , 21 , 29 ) 2E2J 3.5 Sc 10 subunits T/N/R GMPCPP posttranslocation open MD, MSM,QM ( 7a , 16 ) 2O5J 3.0 Tt α 2 ββ′ω T/N/R ATP posttranslocation closed MD ( 18 ) 2PPB 3.0 Tt α 2 ββ′ω T/N/R AMPCPP preinsertion open MD ( 18a , 18b ) 2NVZ 4.3 Sc 10 subunits T/N/R UTP posttranslocation closed QM ( 62 , 73 ) a Sc, Saccharomyces cerevisiae ; Ta, Thermus aquaticus ; T7, Enterobacteria phage T7; Tt, Thermus thermophilus .
PubMed ID is not available.
Published in 2014
Nucleosomes (blue and red) and RNA polymerase II (magenta) models were generated based on PDB accessions 1AOI and 1I6H, respectively.
Publication Year: 2014
Structure of human mitochondrial RNA polymerase elongation complex.
(2013) Nat Struct Mol Biol 20
PubMed: 24096365 | PubMedCentral: null | DOI: 10.1038/nsmb.2683
( d ) Superimposition of RNA–DNA hybrids in elongation complexes of mtRNAP (orange) and RNAP II (PDB 1I6H 33 , grey).
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