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Crystal structure and RNA binding of the Rpb4/Rpb7 subunits of human RNA polymerase II.
(2005) Nucleic Acids Res 33
PubMed: 16282592 | PubMedCentral: PMC1283528 | DOI: 10.1093/nar/gki945
Figure 2 Structures of the M.jannaschii E/F complex (PDB entry 1go3), yeast Rpb4/Rpb7 complex (PDB entry 1wcm) and human Rpb4/Rpb7 complex.
The yeast structure is from the 12-subunit RNAP II complex obtained at 3.8 Å (PDB entry 1wcm) rather than the higher resolution but less complete structure of the isolated heterodimer.
Optimally superimposition of the human Rpb4/Rpb7 heterodimer onto the yeast heterodimer in the 12-subunit RNAP II complex obtained at 3.8 Å (PDB entry 1wcm) results in 282 equivalent Cα atoms that are within 4 Å (r.m.s. separation of 0.66 Å).
The crystal structure of the entire 12-subunits RNAP II from yeast (PDB entry: 1wcm) is shown, with the 10 core subunits colour-coded as in Cramer et al .
Publication Year: 2005
Ancient origin, functional conservation and fast evolution of DNA-dependent RNA polymerase III.
(2006) Nucleic Acids Res 34
PubMed: 16877568 | PubMedCentral: PMC1540719 | DOI: 10.1093/nar/gkl421
Top and front backbone views of RNA polymerase II in S.cerevisiae , prepared with the RASMOL software ( ), using atomic coordinates 1WCM ( 22 ) at the PDB Protein Data Bank.
Publication Year: 2006
Evolution of complex RNA polymerases: the complete archaeal RNA polymerase structure.
(2009) PLoS Biol 7
PubMed: 19419240 | PubMedCentral: PMC2675907 | DOI: 10.1371/journal.pbio.1000102
(B) Stereo view of the docking region of Rpo13 (orange), in light-magenta Rpo5 and in grey Rpo1 with the eukaryotic Rpb5 (violet) and Rpb1 (plum; PDB entry 1WCM) superimposed; rmsd 2.4 Å for 1... 129 Cα equivalences.
Publication Year: 2009
Architecture of the RNA polymerase II-TFIIF complex revealed by cross-linking and mass spectrometry.
(2010) EMBO J 29
PubMed: 20094031 | PubMedCentral: PMC2810376 | DOI: 10.1038/emboj.2009.401
Results MS cross-link analysis of Pol II To test whether we could extend our cross-link analysis to large multi-protein complexes, we analysed the 12-subunit 513 kDa Pol II, for which a crystal struct... re is available (PDB 1WCM) ( Armache et al , 2005 ).
Observed links falling below this limit are in agreement with the X-ray structure of Pol II (PDB 1WCM); observed links exceeding this limit are potentially in conflict with the known structure.
Publication Year: 2010
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
This figure corresponds to the sequence alignments provided as Supplementary Data S1 and is based on the 1WCM PDB coordinates showing the complete twelve-subunit structure of yeast RNAP II ( 11 ), usi... g the Pymol software ( http://www.pymol.org ).
The beginning of a beautiful friendship: cross-linking/mass spectrometry and modelling of proteins and multi-protein complexes.
(2011) J Struct Biol 173
PubMed: 21029779 | PubMedCentral: PMC3043253 | DOI: 10.1016/j.jsb.2010.10.014
We therefore analysed recently ( Chen et al., 2010 ) a large multi-protein complex, the Saccharomyces cerevisiae RNA polymerase II (Pol II), for which a crystal structure had been deposited (PDB 1WCM ... ( Armache et al., 2005 ) that could be used as a reference to check the quality of cross-link data.
(C) Distribution of alpha-carbon distances for lysine pairs in the crystal structure of Pol II (PDB 1WCM ) ( Armache et al., 2005 ) when scaling the distance distribution for all random lysine pairs in the crystal structure to 106 pairs (blue) and when taking the distance measure of those 106 pairs that were observed by cross-linking (red) ( Chen et al., 2010 ).
(C) Homology model of the Tfg1–Tfg2 dimerization domain positioned on the Pol II structure (PDB 1WCM ) with cross-linked residues labelled by proteins and residue number.
Publication Year: 2011
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.
Point mutations in the Rpb9-homologous domain of Rpc11 that impair transcription termination by RNA polymerase III.
(2011) Nucleic Acids Res 39
PubMed: 21450810 | PubMedCentral: PMC3152337 | DOI: 10.1093/nar/gkr182
( C ) The cryoEM structure (EMD-1802) ( 32 ) was fit with the core pol II crystal structure (PDB 1WCM) ( 52 ) lacking the stalk and the C-terminal domain of Rpb9p.
Structural basis of initial RNA polymerase II transcription.
(2011) EMBO J 30
PubMed: 22056778 | PubMedCentral: PMC3243610 | DOI: 10.1038/emboj.2011.396
Diffraction data were collected at 100 K at beamline X06SA of the Swiss Light Source or beamline ID29 of the European Synchrotron Radiation Facility, and structures were solved with molecular replacem... nt using the 12-subunit Pol II structure (1WCM) in program PHASER ( McCoy et al, 2007 ).
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.
Publication Year: 2012
Structural mimicry in transcription regulation of human RNA polymerase II by the DNA helicase RECQL5.
(2013) Nat Struct Mol Biol 20
PubMed: 23748380 | PubMedCentral: PMC3702667 | DOI: 10.1038/nsmb.2596
A crystal structure of yeast Pol II (PDB code 1WCM) and a class average of negatively stained apo Pol II are shown for comparison.
Publication Year: 2013
The yeast prefoldin-like URI-orthologue Bud27 associates with the RSC nucleosome remodeler and modulates transcription.
(2014) Nucleic Acids Res 42
PubMed: 25081216 | PubMedCentral: PMC4150788 | DOI: 10.1093/nar/gku685
Structure modelling Atomic coordinates of the yeast RNA pol II were retrieved from the Protein Data Bank (PDB, RCSB) with the accession number PDB 1WCM, and visualized with the PyMOL program (DeLano S... ientific LLC) ( 23 ).
Publication Year: 2014
Solving the RNA polymerase I structural puzzle.
(2014) Acta Crystallogr D Biol Crystallogr 70
PubMed: 25286842 | PubMedCentral: PMC4188003 | DOI: 10.1107/S1399004714015788
Crystal structures of Pol II were used for initial tests: ten subunits with open (PDB entry 1i3q ) and closed (PDB entry 1i50 ) clamps and 12 subunits (PDB entry 1wcm ) (Cramer et al. , 2001 ▶... ; Kettenberger et al. , 2004 ▶ ).
Since we expected conformational differences between Pol I and Pol II, the Pol II model (PDB entry 1wcm ; Armache et al. , 2005 ▶ ) was divided into five regions similar to the modules described in Cramer et al. (2001 ▶ ) (see § 2 and Fig. 2 ▶ a ) and subjected to sequential molecular replacement.
Figure 2 Molecular replacement leads to an initial model of Pol I. ( a ) Surface representation of the Pol II model (PDB entry 1wcm ) showing the five different regions used in the sequential molecular replacement, with non-included domains in grey.
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