Primary Citation PubMed: 15537538
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Metal A and metal B sites of nuclear RNA polymerases Pol IV and Pol V are required for siRNA-dependent DNA methylation and gene silencing.
(2009) PLoS One 4
PubMed: 19119310 | PubMedCentral: PMC2605557 | DOI: 10.1371/journal.pone.0004110
The table lists amino acids, numbered according to the PDB:1R9T crystal structure for yeast Pol II, and the changes at these positions in NRPD1, NRPE1 or NRPD2.
The image shows the yeast Pol II Rpb1 and Rbp2 subunits (gray) in complex with the dsDNA substrate (black) and RNA product (red) within Protein Data Bank crystal structure 1R9T (Kornberg laboratory).
Publication Year: 2009
A bridge to transcription by RNA polymerase.
(2008) J Biol 7
PubMed: 19090964 | PubMedCentral: PMC2776398 | DOI: 10.1186/jbiol99
BH from the Sce Pol II elongation complex with mismatched substrate (the TL is in the 'out' position away from substrate-addition site in this structure) [PDB: 1r9t ] (teal) [ 5 ].
Publication Year: 2008
Non-canonical DNA transcription enzymes and the conservation of two-barrel RNA polymerases.
(2010) Nucleic Acids Res 38
PubMed: 20360047 | PubMedCentral: PMC2919709 | DOI: 10.1093/nar/gkq201
The corresponding invariant positions are Rpb1 D 479 , D 481 , D 483 and Rpb2-D 837 (red), Rpb1-R 446 , Rpb2-K 979 and Rpb2-K 987 (blue) and Rpb1-P 448 (grey), as taken from PDB 1R9T ( 8 ).
The left and right panel correspond to the NTP entry and addition configurations, respectively, and are based on the PDB 1R9T and 1R9S coordinates ( 8 ).
Crystallographic coordinates were taken from PDB 1R9T ( 8 ).
Publication Year: 2010
Dissection of Pol II trigger loop function and Pol II activity-dependent control of start site selection in vivo.
(2012) PLoS Genet 8
PubMed: 22511879 | PubMedCentral: PMC3325174 | DOI: 10.1371/journal.pgen.1002627
Partially folded TL from PDB 1R9T, containing a mismatched NTP (not shown) is shown in pink.
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
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).
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 ) 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).
( 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).
The DNA (template in blue and non-template in green) in the binding cleft corresponds to the current study whereas the RNA (red) and DNA (blue) in the exit channel corresponds to the elongation complex (PDB ID 1R9T), all represented as cartoon tube.
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 .
Publication Year: 2013
PubMed ID is not available.
Published in 2014
One of those trajectories (UTP3) was following the major A-E pathway (Supplementary Figure S5 and Supplementary Movie S1), and conformation (Figure 2 ) was thought to be the E site state, locating bel... w the E-site NTPs from the crystal structures, but close to one of them (ncATP from 1R9T).
Publication Year: 2014
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