PDBsum entry 1i50

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protein metals Protein-protein interface(s) links
Transcription PDB id
Protein chains
1419 a.a. *
1094 a.a. *
266 a.a. *
215 a.a. *
84 a.a. *
133 a.a. *
122 a.a. *
65 a.a. *
114 a.a. *
46 a.a. *
_ZN ×8
Waters ×78
* Residue conservation analysis
PDB id:
Name: Transcription
Title: RNA polymerase ii crystal form ii at 2.8 a resolution
Structure: DNA-directed RNA polymerase ii largest subunit. Chain: a. Synonym: rpb1. DNA-directed RNA polymerase ii 140kd polypeptide. Chain: b. Synonym: rpb2. DNA-directed RNA polymerase ii 45kd polypeptide. Chain: c. Synonym: rpb3.
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Strain: delta-rpb4. Strain: delta-rpb4
Biol. unit: Decamer (from PQS)
2.80Å     R-factor:   0.229     R-free:   0.282
Authors: P.Cramer,D.A.Bushnell,R.D.Kornberg
Key ref:
P.Cramer et al. (2001). Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution. Science, 292, 1863-1876. PubMed id: 11313498 DOI: 10.1126/science.1059493
23-Feb-01     Release date:   23-Apr-01    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P04050  (RPB1_YEAST) -  DNA-directed RNA polymerase II subunit RPB1
1733 a.a.
1419 a.a.
Protein chain
Pfam   ArchSchema ?
P08518  (RPB2_YEAST) -  DNA-directed RNA polymerase II subunit RPB2
1224 a.a.
1094 a.a.
Protein chain
Pfam   ArchSchema ?
P16370  (RPB3_YEAST) -  DNA-directed RNA polymerase II subunit RPB3
318 a.a.
266 a.a.
Protein chain
Pfam   ArchSchema ?
P20434  (RPAB1_YEAST) -  DNA-directed RNA polymerases I, II, and III subunit RPABC1
215 a.a.
215 a.a.
Protein chain
Pfam   ArchSchema ?
P20435  (RPAB2_YEAST) -  DNA-directed RNA polymerases I, II, and III subunit RPABC2
155 a.a.
84 a.a.
Protein chain
Pfam   ArchSchema ?
P20436  (RPAB3_YEAST) -  DNA-directed RNA polymerases I, II, and III subunit RPABC3
146 a.a.
133 a.a.
Protein chain
Pfam   ArchSchema ?
P27999  (RPB9_YEAST) -  DNA-directed RNA polymerase II subunit RPB9
122 a.a.
122 a.a.
Protein chain
Pfam   ArchSchema ?
P22139  (RPAB5_YEAST) -  DNA-directed RNA polymerases I, II, and III subunit RPABC5
70 a.a.
65 a.a.
Protein chain
Pfam   ArchSchema ?
P38902  (RPB11_YEAST) -  DNA-directed RNA polymerase II subunit RPB11
120 a.a.
114 a.a.
Protein chain
Pfam   ArchSchema ?
P40422  (RPAB4_YEAST) -  DNA-directed RNA polymerases I, II, and III subunit RPABC4
70 a.a.
46 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains A, B: E.C.  - DNA-directed Rna polymerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Nucleoside triphosphate
+ RNA(n)
= diphosphate
+ RNA(n+1)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   7 terms 
  Biological process     transcription, RNA-dependent   14 terms 
  Biochemical function     RNA polymerase II activity     14 terms  


DOI no: 10.1126/science.1059493 Science 292:1863-1876 (2001)
PubMed id: 11313498  
Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution.
P.Cramer, D.A.Bushnell, R.D.Kornberg.
Structures of a 10-subunit yeast RNA polymerase II have been derived from two crystal forms at 2.8 and 3.1 angstrom resolution. Comparison of the structures reveals a division of the polymerase into four mobile modules, including a clamp, shown previously to swing over the active center. In the 2.8 angstrom structure, the clamp is in an open state, allowing entry of straight promoter DNA for the initiation of transcription. Three loops extending from the clamp may play roles in RNA unwinding and DNA rewinding during transcription. A 2.8 angstrom difference Fourier map reveals two metal ions at the active site, one persistently bound and the other possibly exchangeable during RNA synthesis. The results also provide evidence for RNA exit in the vicinity of the carboxyl-terminal repeat domain, coupling synthesis to RNA processing by enzymes bound to this domain.
  Selected figure(s)  
Figure 7.
Fig. 7. Four mobile modules of the Pol II structure. (A) Backbone traces of the core, jaw-lobe, clamp, and shelf modules of the form 1 structure, shown in gray, blue, yellow, and pink, respectively. (B) Changes in the position of the jaw-lobe, clamp, and shelf modules between form 1 (colored) and form 2 structures (gray). The arrows indicate the direction of charges from form 1 to form 2. The core modules in the two crystal forms were superimposed and then omitted for clarity. (C) The view in (B) rotated 90° about a vertical axis. The core and jaw-lobe modules are omitted for clarity. In form 2, the clamp has swung to the left, opening a wider gap between its edge and the wall located further to the right (not shown).
Figure 8.
Fig. 8. Active center. Stereoview from the Rpb2 side toward the clamp. Two metal ions are revealed in a [A]-weighted mF[obs] DF[calc] difference Fourier map (shown for metal B in green, contoured at 3.0 ) and in a Mn2+ anomalous difference Fourier map (shown for metal A in blue, contoured at 4.0 ). This figure was prepared with BOBSCRIPT (85) and MOLSCRIPT (86).
  The above figures are reprinted by permission from the AAAs: Science (2001, 292, 1863-1876) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
23151482 S.Sainsbury, J.Niesser, and P.Cramer (2013).
Structure and function of the initially transcribing RNA polymerase II-TFIIB complex.
  Nature, 493, 437-440.
PDB codes: 4bbr 4bbs
23250061 W.A.Hendrickson (2013).
Evolution of diffraction methods for solving crystal structures.
  Acta Crystallogr A, 69, 51-59.  
23047735 K.Fridman, A.Mader, M.Zwerger, N.Elia, and O.Medalia (2012).
Advances in tomography: probing the molecular architecture of cells.
  Nat Rev Mol Cell Biol, 13, 736-742.  
22820989 M.W.Kellinger, C.X.Song, J.Chong, X.Y.Lu, C.He, and D.Wang (2012).
5-formylcytosine and 5-carboxylcytosine reduce the rate and substrate specificity of RNA polymerase II transcription.
  Nat Struct Mol Biol, 19, 831-833.  
21417597 A.Y.Park, and C.V.Robinson (2011).
Protein-nucleic acid complexes and the role of mass spectrometry in their structure determination.
  Crit Rev Biochem Mol Biol, 46, 152-164.  
21504834 E.Czeko, M.Seizl, C.Augsberger, T.Mielke, and P.Cramer (2011).
Iwr1 directs RNA polymerase II nuclear import.
  Mol Cell, 42, 261-266.  
21419622 F.A.Rey, and W.I.Sundquist (2011).
Macromolecular assemblages.
  Curr Opin Struct Biol, 21, 221-222.  
21386817 F.W.Martinez-Rucobo, S.Sainsbury, A.C.Cheung, and P.Cramer (2011).
Architecture of the RNA polymerase-Spt4/5 complex and basis of universal transcription processivity.
  EMBO J, 30, 1302-1310.
PDB code: 3qqc
21233849 F.Werner, and D.Grohmann (2011).
Evolution of multisubunit RNA polymerases in the three domains of life.
  Nat Rev Microbiol, 9, 85-98.  
21487437 J.N.Kuehner, E.L.Pearson, and C.Moore (2011).
Unravelling the means to an end: RNA polymerase II transcription termination.
  Nat Rev Mol Cell Biol, 12, 283-294.  
21415355 J.Soutourina, S.Wydau, Y.Ambroise, C.Boschiero, and M.Werner (2011).
Direct interaction of RNA polymerase II and mediator required for transcription in vivo.
  Science, 331, 1451-1454.  
21220119 L.A.Lane, C.Fernández-Tornero, M.Zhou, N.Morgner, D.Ptchelkine, U.Steuerwald, A.Politis, D.Lindner, J.Gvozdenovic, A.C.Gavin, C.W.Müller, and C.V.Robinson (2011).
Mass spectrometry reveals stable modules in holo and apo RNA polymerases I and III.
  Structure, 19, 90.  
22081017 L.Bintu, M.Kopaczynska, C.Hodges, L.Lubkowska, M.Kashlev, and C.Bustamante (2011).
The elongation rate of RNA polymerase determines the fate of transcribed nucleosomes.
  Nat Struct Mol Biol, 18, 1394-1399.  
21292158 M.H.Larson, R.Landick, and S.M.Block (2011).
Single-molecule studies of RNA polymerase: one singular sensation, every little step it takes.
  Mol Cell, 41, 249-262.  
21265742 M.Wojtas, B.Peralta, M.Ondiviela, M.Mogni, S.D.Bell, and N.G.Abrescia (2011).
Archaeal RNA polymerase: the influence of the protruding stalk in crystal packing and preliminary biophysical analysis of the Rpo13 subunit.
  Biochem Soc Trans, 39, 25-30.
PDB code: 2y0s
21250781 S.H.Jun, M.J.Reichlen, M.Tajiri, and K.S.Murakami (2011).
Archaeal RNA polymerase and transcription regulation.
  Crit Rev Biochem Mol Biol, 46, 27-40.  
21358628 S.Lefèvre, H.Dumay-Odelot, L.El-Ayoubi, A.Budd, P.Legrand, N.Pinaud, M.Teichmann, and S.Fribourg (2011).
Structure-function analysis of hRPC62 provides insights into RNA polymerase III transcription initiation.
  Nat Struct Mol Biol, 18, 352-358.
PDB codes: 2xub 2xv4
20562828 A.Tupin, M.Gualtieri, J.P.Leonetti, and K.Brodolin (2010).
The transcription inhibitor lipiarmycin blocks DNA fitting into the RNA polymerase catalytic site.
  EMBO J, 29, 2527-2537.  
20967027 C.Fernández-Tornero, B.Böttcher, U.J.Rashid, U.Steuerwald, B.Flörchinger, D.P.Devos, D.Lindner, and C.W.Müller (2010).
Conformational flexibility of RNA polymerase III during transcriptional elongation.
  EMBO J, 29, 3762-3772.  
20419213 C.Uetrecht, R.J.Rose, E.van Duijn, K.Lorenzen, and A.J.Heck (2010).
Ion mobility mass spectrometry of proteins and protein assemblies.
  Chem Soc Rev, 39, 1633-1655.  
20637414 D.Elmlund, R.Davis, and H.Elmlund (2010).
Ab initio structure determination from electron microscopic images of single molecules coexisting in different functional states.
  Structure, 18, 777-786.  
20562026 D.F.Kelly, D.Dukovski, and T.Walz (2010).
Strategy for the use of affinity grids to prepare non-His-tagged macromolecular complexes for single-particle electron microscopy.
  J Mol Biol, 400, 675-681.  
20457751 D.Pupov, N.Miropolskaya, A.Sevostyanova, I.Bass, I.Artsimovitch, and A.Kulbachinskiy (2010).
Multiple roles of the RNA polymerase {beta}' SW2 region in transcription initiation, promoter escape, and RNA elongation.
  Nucleic Acids Res, 38, 5784-5796.  
20448203 D.Wang, G.Zhu, X.Huang, and S.J.Lippard (2010).
X-ray structure and mechanism of RNA polymerase II stalled at an antineoplastic monofunctional platinum-DNA adduct.
  Proc Natl Acad Sci U S A, 107, 9584-9589.
PDB codes: 3m3y 3m4o
19940126 G.A.Kassavetis, P.Prakash, and E.Shim (2010).
The C53/C37 subcomplex of RNA polymerase III lies near the active site and participates in promoter opening.
  J Biol Chem, 285, 2695-2706.  
20360047 G.Ruprich-Robert, and P.Thuriaux (2010).
Non-canonical DNA transcription enzymes and the conservation of two-barrel RNA polymerases.
  Nucleic Acids Res, 38, 4559-4569.  
20088966 H.Koyama, T.Ueda, T.Ito, and K.Sekimizu (2010).
Novel RNA polymerase II mutation suppresses transcriptional fidelity and oxidative stress sensitivity in rpb9Delta yeast.
  Genes Cells, 15, 151-159.  
20033062 J.Eichner, H.T.Chen, L.Warfield, and S.Hahn (2010).
Position of the general transcription factor TFIIF within the RNA polymerase II transcription preinitiation complex.
  EMBO J, 29, 706-716.  
20418102 M.J.Muñoz, la Mata, and A.R.Kornblihtt (2010).
The carboxy terminal domain of RNA polymerase II and alternative splicing.
  Trends Biochem Sci, 35, 497-504.  
  20452941 N.Visa, and P.Percipalle (2010).
Nuclear functions of actin.
  Cold Spring Harb Perspect Biol, 2, a000620.  
20482321 P.Cramer (2010).
Towards molecular systems biology of gene transcription and regulation.
  Biol Chem, 391, 731-735.  
21034443 R.O.Weinzierl (2010).
The nucleotide addition cycle of RNA polymerase is controlled by two molecular hinges in the Bridge Helix domain.
  BMC Biol, 8, 134.  
20040576 S.Grünberg, C.Reich, M.E.Zeller, M.S.Bartlett, and M.Thomm (2010).
Rearrangement of the RNA polymerase subunit H and the lower jaw in archaeal elongation complexes.
  Nucleic Acids Res, 38, 1950-1963.  
21124318 S.Tagami, S.Sekine, T.Kumarevel, N.Hino, Y.Murayama, S.Kamegamori, M.Yamamoto, K.Sakamoto, and S.Yokoyama (2010).
Crystal structure of bacterial RNA polymerase bound with a transcription inhibitor protein.
  Nature, 468, 978-982.
PDB codes: 3aoh 3aoi
19923176 S.Y.Hong, and P.J.Chen (2010).
Phosphorylation of serine 177 of the small hepatitis delta antigen regulates viral antigenomic RNA replication by interacting with the processive RNA polymerase II.
  J Virol, 84, 1430-1438.  
20483995 T.J.Gries, W.S.Kontur, M.W.Capp, R.M.Saecker, and M.T.Record (2010).
One-step DNA melting in the RNA polymerase cleft opens the initiation bubble to form an unstable open complex.
  Proc Natl Acad Sci U S A, 107, 10418-10423.  
20158916 T.Marcussen, B.Oxelman, A.Skog, and K.S.Jakobsen (2010).
Evolution of plant RNA polymerase IV/V genes: evidence of subneofunctionalization of duplicated NRPD2/NRPE2-like paralogs in Viola (Violaceae).
  BMC Evol Biol, 10, 45.  
19895816 W.J.Lane, and S.A.Darst (2010).
Molecular evolution of multisubunit RNA polymerases: structural analysis.
  J Mol Biol, 395, 686-704.  
19895820 W.J.Lane, and S.A.Darst (2010).
Molecular evolution of multisubunit RNA polymerases: sequence analysis.
  J Mol Biol, 395, 671-685.  
20116858 X.Li, S.A.Hayik, and K.M.Merz (2010).
QM/MM X-ray refinement of zinc metalloenzymes.
  J Inorg Biochem, 104, 512-522.  
20094031 Z.A.Chen, A.Jawhari, L.Fischer, C.Buchen, S.Tahir, T.Kamenski, M.Rasmussen, L.Lariviere, J.C.Bukowski-Wills, M.Nilges, P.Cramer, and J.Rappsilber (2010).
Architecture of the RNA polymerase II-TFIIF complex revealed by cross-linking and mass spectrometry.
  EMBO J, 29, 717-726.  
20567074 Z.Dauter, M.Jaskolski, and A.Wlodawer (2010).
Impact of synchrotron radiation on macromolecular crystallography: a personal view.
  J Synchrotron Radiat, 17, 433-444.  
19880312 A.Hirata, and K.S.Murakami (2009).
Archaeal RNA polymerase.
  Curr Opin Struct Biol, 19, 724-731.  
19717427 A.Korkut, and W.A.Hendrickson (2009).
A force field for virtual atom molecular mechanics of proteins.
  Proc Natl Acad Sci U S A, 106, 15667-15672.  
19903881 B.P.Hudson, J.Quispe, S.Lara-González, Y.Kim, H.M.Berman, E.Arnold, R.H.Ebright, and C.L.Lawson (2009).
Three-dimensional EM structure of an intact activator-dependent transcription initiation complex.
  Proc Natl Acad Sci U S A, 106, 19830-19835.
PDB code: 3iyd
19183282 C.Reich, M.Zeller, P.Milkereit, W.Hausner, P.Cramer, H.Tschochner, and M.Thomm (2009).
The archaeal RNA polymerase subunit P and the eukaryotic polymerase subunit Rpb12 are interchangeable in vivo and in vitro.
  Mol Microbiol, 71, 989.  
20004159 C.W.Carter (2009).
E pluribus tres: the 2009 nobel prize in chemistry.
  Structure, 17, 1558-1561.  
19439405 C.Walmacq, M.L.Kireeva, J.Irvin, Y.Nedialkov, L.Lubkowska, F.Malagon, J.N.Strathern, and M.Kashlev (2009).
Rpb9 subunit controls transcription fidelity by delaying NTP sequestration in RNA polymerase II.
  J Biol Chem, 284, 19601-19612.  
19109435 C.Y.Chen, C.C.Chang, C.F.Yen, M.T.Chiu, and W.H.Chang (2009).
Mapping RNA exit channel on transcribing RNA polymerase II by FRET analysis.
  Proc Natl Acad Sci U S A, 106, 127-132.  
19820686 D.Kostrewa, M.E.Zeller, K.J.Armache, M.Seizl, K.Leike, M.Thomm, and P.Cramer (2009).
RNA polymerase II-TFIIB structure and mechanism of transcription initiation.
  Nature, 462, 323-330.
PDB code: 3k1f
19489723 E.Nudler (2009).
RNA polymerase active center: the molecular engine of transcription.
  Annu Rev Biochem, 78, 335-361.  
19481445 F.Brueckner, J.Ortiz, and P.Cramer (2009).
A movie of the RNA polymerase nucleotide addition cycle.
  Curr Opin Struct Biol, 19, 294-299.  
19171965 F.Brueckner, K.J.Armache, A.Cheung, G.E.Damsma, H.Kettenberger, E.Lehmann, J.Sydow, and P.Cramer (2009).
Structure-function studies of the RNA polymerase II elongation complex.
  Acta Crystallogr D Biol Crystallogr, 65, 112-120.  
18946472 G.A.Belogurov, M.N.Vassylyeva, A.Sevostyanova, J.R.Appleman, A.X.Xiang, R.Lira, S.E.Webber, S.Klyuyev, E.Nudler, I.Artsimovitch, and D.G.Vassylyev (2009).
Transcription inactivation through local refolding of the RNA polymerase structure.
  Nature, 457, 332-335.
PDB code: 3eql
19647516 H.Saeki, and J.Q.Svejstrup (2009).
Stability, flexibility, and dynamic interactions of colliding RNA polymerase II elongation complexes.
  Mol Cell, 35, 191-205.  
19458260 H.Spåhr, G.Calero, D.A.Bushnell, and R.D.Kornberg (2009).
Schizosacharomyces pombe RNA polymerase II at 3.6-A resolution.
  Proc Natl Acad Sci U S A, 106, 9185-9190.
PDB code: 3h0g
19620213 J.Andrecka, B.Treutlein, M.A.Arcusa, A.Muschielok, R.Lewis, A.C.Cheung, P.Cramer, and J.Michaelis (2009).
Nano positioning system reveals the course of upstream and nontemplate DNA within the RNA polymerase II elongation complex.
  Nucleic Acids Res, 37, 5803-5809.  
19936246 J.L.Stonaker, J.P.Lim, K.F.Erhard, and J.B.Hollick (2009).
Diversity of Pol IV function is defined by mutations at the maize rmr7 locus.
  PLoS Genet, 5, e1000706.  
19119310 J.R.Haag, O.Pontes, and C.S.Pikaard (2009).
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.
  PLoS ONE, 4, e4110.  
  19478915 J.Wang, I.Dasgupta, and G.E.Fox (2009).
Many nonuniversal archaeal ribosomal proteins are found in conserved gene clusters.
  Archaea, 2, 241-251.  
19936058 L.Sidorenko, J.E.Dorweiler, A.M.Cigan, M.Arteaga-Vazquez, M.Vyas, J.Kermicle, D.Jurcin, J.Brzeski, Y.Cai, and V.L.Chandler (2009).
A dominant mutation in mediator of paramutation2, one of three second-largest subunits of a plant-specific RNA polymerase, disrupts multiple siRNA silencing processes.
  PLoS Genet, 5, e1000725.  
19903202 M.Sakamoto, S.Noguchi, S.Kawashima, Y.Okada, T.Enomoto, M.Seki, and M.Horikoshi (2009).
Global analysis of mutual interaction surfaces of nucleosomes with comprehensive point mutants.
  Genes Cells, 14, 1271-1330.  
19926275 M.X.Ho, B.P.Hudson, K.Das, E.Arnold, and R.H.Ebright (2009).
Structures of RNA polymerase-antibiotic complexes.
  Curr Opin Struct Biol, 19, 715-723.  
19590095 N.E.Thompson, B.T.Glaser, K.M.Foley, Z.F.Burton, and R.R.Burgess (2009).
Minimal promoter systems reveal the importance of conserved residues in the B-finger of human transcription factor IIB.
  J Biol Chem, 284, 24754-24766.  
19855007 N.Miropolskaya, I.Artsimovitch, S.Klimasauskas, V.Nikiforov, and A.Kulbachinskiy (2009).
Allosteric control of catalysis by the F loop of RNA polymerase.
  Proc Natl Acad Sci U S A, 106, 18942-18947.  
19289466 P.A.Meyer, P.Ye, M.H.Suh, M.Zhang, and J.Fu (2009).
Structure of the 12-subunit RNA polymerase II refined with the aid of anomalous diffraction data.
  J Biol Chem, 284, 12933-12939.
PDB code: 3fki
19924201 S.Hahn (2009).
Structural biology: New beginnings for transcription.
  Nature, 462, 292-293.  
  19838335 S.Imamura, and M.Asayama (2009).
Sigma factors for cyanobacterial transcription.
  Gene Regul Syst Bio, 3, 65-87.  
19141635 S.Lahmy, D.Pontier, E.Cavel, D.Vega, M.El-Shami, T.Kanno, and T.Lagrange (2009).
PolV(PolIVb) function in RNA-directed DNA methylation requires the conserved active site and an additional plant-specific subunit.
  Proc Natl Acad Sci U S A, 106, 941-946.  
19171784 S.T.Rutherford, C.L.Villers, J.H.Lee, W.Ross, and R.L.Gourse (2009).
Allosteric control of Escherichia coli rRNA promoter complexes by DksA.
  Genes Dev, 23, 236-248.  
19110459 T.S.Ream, J.R.Haag, A.T.Wierzbicki, C.D.Nicora, A.D.Norbeck, J.K.Zhu, G.Hagen, T.J.Guilfoyle, L.Pasa-Tolić, and C.S.Pikaard (2009).
Subunit compositions of the RNA-silencing enzymes Pol IV and Pol V reveal their origins as specialized forms of RNA polymerase II.
  Mol Cell, 33, 192-203.  
19595716 V.K.Gangaraju, P.Prasad, A.Srour, M.N.Kagalwala, and B.Bartholomew (2009).
Conformational changes associated with template commitment in ATP-dependent chromatin remodeling by ISW2.
  Mol Cell, 35, 58-69.  
19079241 W.N.Price, Y.Chen, S.K.Handelman, H.Neely, P.Manor, R.Karlin, R.Nair, J.Liu, M.Baran, J.Everett, S.N.Tong, F.Forouhar, S.S.Swaminathan, T.Acton, R.Xiao, J.R.Luft, A.Lauricella, G.T.DeTitta, B.Rost, G.T.Montelione, and J.F.Hunt (2009).
Understanding the physical properties that control protein crystallization by analysis of large-scale experimental data.
  Nat Biotechnol, 27, 51-57.  
19419240 Y.Korkhin, U.M.Unligil, O.Littlefield, P.J.Nelson, D.I.Stuart, P.B.Sigler, S.D.Bell, and N.G.Abrescia (2009).
Evolution of Complex RNA Polymerases: The Complete Archaeal RNA Polymerase Structure.
  PLoS Biol, 7, e102.
PDB codes: 2waq 2wb1
19915655 A.Bashan, and A.Yonath (2008).
The linkage between ribosomal crystallography, metal ions, heteropolytungstates and functional flexibility.
  J Mol Struct, 890, 289-294.  
18022639 A.Dimitri, A.K.Goodenough, F.P.Guengerich, S.Broyde, and D.A.Scicchitano (2008).
Transcription processing at 1,N2-ethenoguanine by human RNA polymerase II and bacteriophage T7 RNA polymerase.
  J Mol Biol, 375, 353-366.  
18854351 A.Dimitri, J.A.Burns, S.Broyde, and D.A.Scicchitano (2008).
Transcription elongation past O6-methylguanine by human RNA polymerase II and bacteriophage T7 RNA polymerase.
  Nucleic Acids Res, 36, 6459-6471.  
18555749 A.Dimitri, L.Jia, V.Shafirovich, N.E.Geacintov, S.Broyde, and D.A.Scicchitano (2008).
Transcription of DNA containing the 5-guanidino-4-nitroimidazole lesion by human RNA polymerase II and bacteriophage T7 RNA polymerase.
  DNA Repair (Amst), 7, 1276-1288.  
18235446 A.Hirata, B.J.Klein, and K.S.Murakami (2008).
The X-ray crystal structure of RNA polymerase from Archaea.
  Nature, 451, 851-854.
PDB codes: 2pa8 2pmz 3hkz
18974734 A.J.Heck (2008).
Native mass spectrometry: a bridge between interactomics and structural biology.
  Nat Methods, 5, 927-933.  
18849988 A.Muschielok, J.Andrecka, A.Jawhari, F.Brückner, P.Cramer, and J.Michaelis (2008).
A nano-positioning system for macromolecular structural analysis.
  Nat Methods, 5, 965-971.  
18264749 B.A.Knutson, and S.S.Broyles (2008).
Expansion of poxvirus RNA polymerase subunits sharing homology with corresponding subunits of RNA polymerase II.
  Virus Genes, 36, 307-311.  
18832375 B.Cheng, and D.H.Price (2008).
Analysis of factor interactions with RNA polymerase II elongation complexes using a new electrophoretic mobility shift assay.
  Nucleic Acids Res, 36, e135.  
18922021 C.D.Amero, W.P.Boomershine, Y.Xu, and M.Foster (2008).
Solution structure of Pyrococcus furiosus RPP21, a component of the archaeal RNase P holoenzyme, and interactions with its RPP29 protein partner.
  Biochemistry, 47, 11704-11710.
PDB code: 2k3r
18538653 C.D.Kaplan, K.M.Larsson, and R.D.Kornberg (2008).
The RNA polymerase II trigger loop functions in substrate selection and is directly targeted by alpha-amanitin.
  Mol Cell, 30, 547-556.
PDB code: 3cqz
18158581 C.R.Mandel, Y.Bai, and L.Tong (2008).
Protein factors in pre-mRNA 3'-end processing.
  Cell Mol Life Sci, 65, 1099-1122.  
18362165 D.A.Khaperskyy, M.L.Ammerman, R.C.Majovski, and A.S.Ponticelli (2008).
Functions of Saccharomyces cerevisiae TFIIF during transcription start site utilization.
  Mol Cell Biol, 28, 3757-3766.  
18713742 E.Bitto, C.A.Bingman, L.Bittova, D.A.Kondrashov, R.M.Bannen, B.G.Fox, J.L.Markley, and G.N.Phillips (2008).
Structure of human J-type co-chaperone HscB reveals a tetracysteine metal-binding domain.
  J Biol Chem, 283, 30184-30192.
PDB code: 3bvo
18086878 F.Beckouet, S.Labarre-Mariotte, B.Albert, Y.Imazawa, M.Werner, O.Gadal, Y.Nogi, and P.Thuriaux (2008).
Two RNA polymerase I subunits control the binding and release of Rrn3 during transcription.
  Mol Cell Biol, 28, 1596-1605.  
18552824 F.Brueckner, and P.Cramer (2008).
Structural basis of transcription inhibition by alpha-amanitin and implications for RNA polymerase II translocation.
  Nat Struct Mol Biol, 15, 811-818.
PDB code: 2vum
18678648 F.Malagon, and T.H.Jensen (2008).
The T body, a new cytoplasmic RNA granule in Saccharomyces cerevisiae.
  Mol Cell Biol, 28, 6022-6032.  
18940870 F.Xiao, H.Zhang, and P.Guo (2008).
Novel mechanism of hexamer ring assembly in protein/RNA interactions revealed by single molecule imaging.
  Nucleic Acids Res, 36, 6620-6632.  
18162559 J.Andrecka, R.Lewis, F.Brückner, E.Lehmann, P.Cramer, and J.Michaelis (2008).
Single-molecule tracking of mRNA exiting from RNA polymerase II.
  Proc Natl Acad Sci U S A, 105, 135-140.  
19004804 J.Bockhorn, B.Balar, D.He, E.Seitomer, P.R.Copeland, and T.G.Kinzy (2008).
Genome-wide screen of Saccharomyces cerevisiae null allele strains identifies genes involved in selenomethionine resistance.
  Proc Natl Acad Sci U S A, 105, 17682-17687.  
18084032 J.Gerber, A.Reiter, R.Steinbauer, S.Jakob, C.D.Kuhn, P.Cramer, J.Griesenbeck, P.Milkereit, and H.Tschochner (2008).
Site specific phosphorylation of yeast RNA polymerase I.
  Nucleic Acids Res, 36, 793-802.  
18846104 J.L.Corden (2008).
Yeast Pol II start-site selection: the long and the short of it.
  EMBO Rep, 9, 1084-1086.  
18957204 J.Mukhopadhyay, K.Das, S.Ismail, D.Koppstein, M.Jang, B.Hudson, S.Sarafianos, S.Tuske, J.Patel, R.Jansen, H.Irschik, E.Arnold, and R.H.Ebright (2008).
The RNA polymerase "switch region" is a target for inhibitors.
  Cell, 135, 295-307.
PDB code: 3dxj
18657503 J.N.Kuehner, and D.A.Brow (2008).
Regulation of a eukaryotic gene by GTP-dependent start site selection and transcription attenuation.
  Mol Cell, 31, 201-211.  
18949821 K.Baranes-Bachar, K.Baranes-Bacher, I.Khalaila, Y.Ivantsiv, A.Lavut, O.Voloshin, and D.Raveh (2008).
New interacting partners of the F-box protein Ufo1 of yeast.
  Yeast, 25, 733-743.  
18187511 K.Kasahara, S.Ki, K.Aoyama, H.Takahashi, and T.Kokubo (2008).
Saccharomyces cerevisiae HMO1 interacts with TFIID and participates in start site selection by RNA polymerase II.
  Nucleic Acids Res, 36, 1343-1357.  
18410247 K.M.Herbert, W.J.Greenleaf, and S.M.Block (2008).
Single-molecule studies of RNA polymerase: motoring along.
  Annu Rev Biochem, 77, 149-176.  
19055851 L.Tan, S.Wiesler, D.Trzaska, H.C.Carney, and R.O.Weinzierl (2008).
Bridge helix and trigger loop perturbations generate superactive RNA polymerases.
  J Biol, 7, 40.  
18166977 M.Fousteri, and L.H.Mullenders (2008).
Transcription-coupled nucleotide excision repair in mammalian cells: molecular mechanisms and biological effects.
  Cell Res, 18, 73-84.  
18426909 M.H.Jenks, T.W.O'Rourke, and D.Reines (2008).
Properties of an intergenic terminator and start site switch that regulate IMD2 transcription in yeast.
  Mol Cell Biol, 28, 3883-3893.  
18982294 M.Kvaratskhelia, and S.F.Grice (2008).
Structural analysis of protein-RNA interactions with mass spectrometry.
  Methods Mol Biol, 488, 213-219.  
18384908 M.Kwapisz, F.Beckouët, and P.Thuriaux (2008).
Early evolution of eukaryotic DNA-dependent RNA polymerases.
  Trends Genet, 24, 211-215.  
18716630 M.Kwapisz, M.Wery, D.Després, Y.Ghavi-Helm, J.Soutourina, P.Thuriaux, and F.Lacroute (2008).
Mutations of RNA polymerase II activate key genes of the nucleoside triphosphate biosynthetic pathways.
  EMBO J, 27, 2411-2421.  
18538654 M.L.Kireeva, Y.A.Nedialkov, G.H.Cremona, Y.A.Purtov, L.Lubkowska, F.Malagon, Z.F.Burton, J.N.Strathern, and M.Kashlev (2008).
Transient reversal of RNA polymerase II active site closing controls fidelity of transcription elongation.
  Mol Cell, 30, 557-566.  
18597481 M.Morar, A.A.Hoskins, J.Stubbe, and S.E.Ealick (2008).
Formylglycinamide ribonucleotide amidotransferase from Thermotoga maritima: structural insights into complex formation.
  Biochemistry, 47, 7816-7830.
PDB code: 3d54
18417719 M.Naito, K.Bomsztyk, and R.A.Zager (2008).
Endotoxin mediates recruitment of RNA polymerase II to target genes in acute renal failure.
  J Am Soc Nephrol, 19, 1321-1330.  
18354501 M.Okuda, A.Tanaka, M.Satoh, S.Mizuta, M.Takazawa, Y.Ohkuma, and Y.Nishimura (2008).
Structural insight into the TFIIE-TFIIH interaction: TFIIE and p53 share the binding region on TFIIH.
  EMBO J, 27, 1161-1171.
PDB codes: 2rnq 2rnr
18408053 P.A.Gibney, T.Fries, S.M.Bailer, and K.A.Morano (2008).
Rtr1 is the Saccharomyces cerevisiae homolog of a novel family of RNA polymerase II-binding proteins.
  Eukaryot Cell, 7, 938-948.  
18573085 P.Cramer, K.J.Armache, S.Baumli, S.Benkert, F.Brueckner, C.Buchen, G.E.Damsma, S.Dengl, S.R.Geiger, A.J.Jasiak, A.Jawhari, S.Jennebach, T.Kamenski, H.Kettenberger, C.D.Kuhn, E.Lehmann, K.Leike, J.F.Sydow, and A.Vannini (2008).
Structure of eukaryotic RNA polymerases.
  Annu Rev Biophys, 37, 337-352.  
18599813 P.J.Lewis, G.P.Doherty, and J.Clarke (2008).
Transcription factor dynamics.
  Microbiology, 154, 1837-1844.  
18427828 R.Luna, H.Gaillard, C.González-Aguilera, and A.Aguilera (2008).
Biogenesis of mRNPs: integrating different processes in the eukaryotic nucleus.
  Chromosoma, 117, 319-331.  
18280161 S.Borukhov, and E.Nudler (2008).
RNA polymerase: the vehicle of transcription.
  Trends Microbiol, 16, 126-134.  
18073196 S.Naji, M.G.Bertero, P.Spitalny, P.Cramer, and M.Thomm (2008).
Structure-function analysis of the RNA polymerase cleft loops elucidates initial transcription, DNA unwinding and RNA displacement.
  Nucleic Acids Res, 36, 676-687.  
18025041 S.Nottebaum, L.Tan, D.Trzaska, H.C.Carney, and R.O.Weinzierl (2008).
The RNA polymerase factory: a robotic in vitro assembly platform for high-throughput production of recombinant protein complexes.
  Nucleic Acids Res, 36, 245-252.  
18521075 S.P.Haugen, W.Ross, and R.L.Gourse (2008).
Advances in bacterial promoter recognition and its control by factors that do not bind DNA.
  Nat Rev Microbiol, 6, 507-519.  
17636315 A.Pombo (2007).
Advances in imaging the interphase nucleus using thin cryosections.
  Histochem Cell Biol, 128, 97.  
17342411 A.Siddiq, L.R.Aminova, and R.R.Ratan (2007).
Hypoxia inducible factor prolyl 4-hydroxylase enzymes: center stage in the battle against hypoxia, metabolic compromise and oxidative stress.
  Neurochem Res, 32, 931-946.  
17418786 B.P.Somesh, S.Sigurdsson, H.Saeki, H.Erdjument-Bromage, P.Tempst, and J.Q.Svejstrup (2007).
Communication between distant sites in RNA polymerase II through ubiquitylation factors and the polymerase CTD.
  Cell, 129, 57-68.  
17623850 B.Tamames, S.F.Sousa, J.Tamames, P.A.Fernandes, and M.J.Ramos (2007).
Analysis of zinc-ligand bond lengths in metalloproteins: trends and patterns.
  Proteins, 69, 466-475.  
18160037 C.D.Kuhn, S.R.Geiger, S.Baumli, M.Gartmann, J.Gerber, S.Jennebach, T.Mielke, H.Tschochner, R.Beckmann, and P.Cramer (2007).
Functional architecture of RNA polymerase I.
  Cell, 131, 1260-1272.
PDB code: 2rf4
17386259 C.Fernández-Tornero, B.Böttcher, M.Riva, C.Carles, U.Steuerwald, R.W.Ruigrok, A.Sentenac, C.W.Müller, and G.Schoehn (2007).
Insights into transcription initiation and termination from the electron microscopy structure of yeast RNA polymerase III.
  Mol Cell, 25, 813-823.  
17983264 C.H.Yeang, and D.Haussler (2007).
Detecting coevolution in and among protein domains.
  PLoS Comput Biol, 3, e211.  
17287347 C.Hyeon, and J.N.Onuchic (2007).
Internal strain regulates the nucleotide binding site of the kinesin leading head.
  Proc Natl Acad Sci U S A, 104, 2175-2180.  
17179178 C.Zaros, J.F.Briand, Y.Boulard, S.Labarre-Mariotte, M.C.Garcia-Lopez, P.Thuriaux, and F.Navarro (2007).
Functional organization of the Rpb5 subunit shared by the three yeast RNA polymerases.
  Nucleic Acids Res, 35, 634-647.  
17466624 D.A.Schneider, A.Michel, M.L.Sikes, L.Vu, J.A.Dodd, S.Salgia, Y.N.Osheim, A.L.Beyer, and M.Nomura (2007).
Transcription elongation by RNA polymerase I is linked to efficient rRNA processing and ribosome assembly.
  Mol Cell, 26, 217-229.  
17581590 D.G.Vassylyev, M.N.Vassylyeva, A.Perederina, T.H.Tahirov, and I.Artsimovitch (2007).
Structural basis for transcription elongation by bacterial RNA polymerase.
  Nature, 448, 157-162.
PDB code: 2o5i
18081935 E.V.Koonin, K.S.Makarova, and J.G.Elkins (2007).
Orthologs of the small RPB8 subunit of the eukaryotic RNA polymerases are conserved in hyperthermophilic Crenarchaeota and "Korarchaeota".
  Biol Direct, 2, 38.  
18007667 G.Melino, P.Nicotera, and G.Macino (2007).
In the beginning there was RNA, then came transcription regulation: the Nobel Prize Lectures 2006.
  Cell Death Differ, 14, 1975-1976.  
17868464 H.Wang, E.Segal, A.Ben-Hur, Q.R.Li, M.Vidal, and D.Koller (2007).
InSite: a computational method for identifying protein-protein interaction binding sites on a proteome-wide scale.
  Genome Biol, 8, R192.  
17679091 I.Toulokhonov, J.Zhang, M.Palangat, and R.Landick (2007).
A central role of the RNA polymerase trigger loop in active-site rearrangement during transcriptional pausing.
  Mol Cell, 27, 406-419.  
17411433 J.B.Pereira-Leal, E.D.Levy, C.Kamp, and S.A.Teichmann (2007).
Evolution of protein complexes by duplication of homomeric interactions.
  Genome Biol, 8, R51.  
17160640 J.Luo, and B.D.Hall (2007).
A multistep process gave rise to RNA polymerase IV of land plants.
  J Mol Evol, 64, 101-112.  
18160031 J.R.Haag, and C.S.Pikaard (2007).
RNA polymerase I: a multifunctional molecular machine.
  Cell, 131, 1224-1225.  
17937913 K.Lorenzen, A.Vannini, P.Cramer, and A.J.Heck (2007).
Structural biology of RNA polymerase III: mass spectrometry elucidates subcomplex architecture.
  Structure, 15, 1237-1245.  
17339209 L.Peiró-Chova, and F.Estruch (2007).
Specific defects in different transcription complexes compensate for the requirement of the negative cofactor 2 repressor in Saccharomyces cerevisiae.
  Genetics, 176, 125-138.  
17101794 M.Reyes-Reyes, and M.Hampsey (2007).
Role for the Ssu72 C-terminal domain phosphatase in RNA polymerase II transcription elongation.
  Mol Cell Biol, 27, 926-936.  
17202208 M.S.Almeida, M.A.Johnson, T.Herrmann, M.Geralt, and K.Wüthrich (2007).
Novel beta-barrel fold in the nuclear magnetic resonance structure of the replicase nonstructural protein 1 from the severe acute respiratory syndrome coronavirus.
  J Virol, 81, 3151-3161.
PDB codes: 2gdt 2hsx
17351896 M.W.Lee, B.J.Kim, H.K.Choi, M.J.Ryu, S.B.Kim, K.M.Kang, E.J.Cho, H.D.Youn, W.K.Huh, and S.T.Kim (2007).
Global protein expression profiling of budding yeast in response to DNA damage.
  Yeast, 24, 145-154.  
18044988 N.S.Yee, W.Gong, Y.Huang, K.Lorent, A.C.Dolan, R.J.Maraia, and M.Pack (2007).
Mutation of RNA Pol III subunit rpc2/polr3b Leads to Deficiency of Subunit Rpc11 and disrupts zebrafish digestive development.
  PLoS Biol, 5, e312.  
17565764 O.Schiemann, and T.F.Prisner (2007).
Long-range distance determinations in biomacromolecules by EPR spectroscopy.
  Q Rev Biophys, 40, 1.  
17676030 P.Cramer (2007).
Finding the right spot to start transcription.
  Nat Struct Mol Biol, 14, 686-687.  
17625551 P.Cramer (2007).
Gene transcription: extending the message.
  Nature, 448, 142-143.  
17670940 R.D.Kornberg (2007).
The molecular basis of eukaryotic transcription.
  Proc Natl Acad Sci U S A, 104, 12955-12961.  
17253774 R.S.Turingan, C.Liu, M.E.Hawkins, and C.T.Martin (2007).
Structural confirmation of a bent and open model for the initiation complex of T7 RNA polymerase.
  Biochemistry, 46, 1714-1723.  
17336362 S.G.Cresawn, C.Prins, D.R.Latner, and R.C.Condit (2007).
Mapping and phenotypic analysis of spontaneous isatin-beta-thiosemicarbazone resistant mutants of vaccinia virus.
  Virology, 363, 319-332.  
17452455 X.Chen, C.Ruggiero, and S.Li (2007).
Yeast Rpb9 plays an important role in ubiquitylation and degradation of Rpb1 in response to UV-induced DNA damage.
  Mol Cell Biol, 27, 4617-4625.  
17676063 X.Darzacq, Y.Shav-Tal, Turris, Y.Brody, S.M.Shenoy, R.D.Phair, and R.H.Singer (2007).
In vivo dynamics of RNA polymerase II transcription.
  Nat Struct Mol Biol, 14, 796-806.  
18006688 Y.X.Xu, and J.L.Manley (2007).
Pin1 modulates RNA polymerase II activity during the transcription cycle.
  Genes Dev, 21, 2950-2962.  
16818233 A.J.Jasiak, K.J.Armache, B.Martens, R.P.Jansen, and P.Cramer (2006).
Structural biology of RNA polymerase III: subcomplex C17/25 X-ray structure and 11 subunit enzyme model.
  Mol Cell, 23, 71-81.
PDB code: 2ckz
16327806 A.Ujvári, and D.S.Luse (2006).
RNA emerging from the active site of RNA polymerase II interacts with the Rpb7 subunit.
  Nat Struct Mol Biol, 13, 49-54.  
17381329 C.S.Pikaard (2006).
Cell biology of the Arabidopsis nuclear siRNA pathway for RNA-directed chromatin modification.
  Cold Spring Harb Symp Quant Biol, 71, 473-480.  
17129781 D.Wang, D.A.Bushnell, K.D.Westover, C.D.Kaplan, and R.D.Kornberg (2006).
Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis.
  Cell, 127, 941-954.
PDB codes: 2e2h 2e2i 2e2j 2nvq 2nvs 2nvt 2nvx 2nvy 2nvz 2yu9
16537912 E.J.Steinmetz, S.B.Ng, J.P.Cloute, and D.A.Brow (2006).
cis- and trans-Acting determinants of transcription termination by yeast RNA polymerase II.
  Mol Cell Biol, 26, 2688-2696.  
17052459 E.Kashkina, M.Anikin, F.Brueckner, R.T.Pomerantz, W.T.McAllister, P.Cramer, and D.Temiakov (2006).
Template misalignment in multisubunit RNA polymerases and transcription fidelity.
  Mol Cell, 24, 257-266.  
16510790 F.Malagon, M.L.Kireeva, B.K.Shafer, L.Lubkowska, M.Kashlev, and J.N.Strathern (2006).
Mutations in the Saccharomyces cerevisiae RPB1 gene conferring hypersensitivity to 6-azauracil.
  Genetics, 172, 2201-2209.  
16689630 F.Tama, and C.L.Brooks (2006).
Symmetry, form, and shape: guiding principles for robustness in macromolecular machines.
  Annu Rev Biophys Biomol Struct, 35, 115-133.  
16819517 G.Miller, and S.Hahn (2006).
A DNA-tethered cleavage probe reveals the path for promoter DNA in the yeast preinitiation complex.
  Nat Struct Mol Biol, 13, 603-610.  
16341226 H.Kettenberger, A.Eisenführ, F.Brueckner, M.Theis, M.Famulok, and P.Cramer (2006).
Structure of an RNA polymerase II-RNA inhibitor complex elucidates transcription regulation by noncoding RNAs.
  Nat Struct Mol Biol, 13, 44-48.
PDB code: 2b63
16421445 H.Kettenberger, and P.Cramer (2006).
Fluorescence detection of nucleic acids and proteins in multi-component crystals.
  Acta Crystallogr D Biol Crystallogr, 62, 146-150.  
16495046 I.Grummt (2006).
Actin and myosin as transcription factors.
  Curr Opin Genet Dev, 16, 191-196.  
16713251 J.Bravo, and P.Aloy (2006).
Target selection for complex structural genomics.
  Curr Opin Struct Biol, 16, 385-392.  
17205138 J.H.Reina, T.N.Azzouz, and N.Hernandez (2006).
Maf1, a new player in the regulation of human RNA polymerase III transcription.
  PLoS ONE, 1, e134.  
16724108 J.Thompson, T.Lepikhova, N.Teixido-Travesa, M.A.Whitehead, J.J.Palvimo, and O.A.Jänne (2006).
Small carboxyl-terminal domain phosphatase 2 attenuates androgen-dependent transcription.
  EMBO J, 25, 2757-2767.  
16765888 J.Zlatanova, W.T.McAllister, S.Borukhov, and S.H.Leuba (2006).
Single-molecule approaches reveal the idiosyncrasies of RNA polymerases.
  Structure, 14, 953-966.  
16809778 K.I.Panov, T.B.Panova, O.Gadal, K.Nishiyama, T.Saito, J.Russell, and J.C.Zomerdijk (2006).
RNA polymerase I-specific subunit CAST/hPAF49 has a role in the activation of transcription by upstream binding factor.
  Mol Cell Biol, 26, 5436-5448.  
16758199 M.Hallberg, G.Z.Hu, S.Tronnersjö, Z.Shaikhibrahim, D.Balciunas, S.Björklund, and H.Ronne (2006).
Functional and physical interactions within the middle domain of the yeast mediator.
  Mol Genet Genomics, 276, 197-210.  
16826228 M.Hampsey (2006).
The Pol II initiation complex: finding a place to start.
  Nat Struct Mol Biol, 13, 564-566.  
16461361 M.Hoshino, M.L.Qi, N.Yoshimura, T.Miyashita, K.Tagawa, Y.Wada, Y.Enokido, S.Marubuchi, P.Harjes, N.Arai, K.Oyanagi, G.Blandino, M.Sudol, T.Rich, I.Kanazawa, E.E.Wanker, M.Saitoe, and H.Okazawa (2006).
Transcriptional repression induces a slowly progressive atypical neuronal death associated with changes of YAP isoforms and p73.
  J Cell Biol, 172, 589-604.  
16640457 M.J.Hicks, C.R.Yang, M.V.Kotlajich, and K.J.Hertel (2006).
Linking splicing to Pol II transcription stabilizes pre-mRNAs and influences splicing patterns.
  PLoS Biol, 4, e147.  
16492753 N.K.Nesser, D.O.Peterson, and D.K.Hawley (2006).
RNA polymerase II subunit Rpb9 is important for transcriptional fidelity in vivo.
  Proc Natl Acad Sci U S A, 103, 3268-3273.  
16581837 O.Coban, D.C.Lamb, E.Zaychikov, H.Heumann, and G.U.Nienhaus (2006).
Conformational heterogeneity in RNA polymerase observed by single-pair FRET microscopy.
  Biophys J, 90, 4605-4617.  
16765890 P.A.Meyer, P.Ye, M.Zhang, M.H.Suh, and J.Fu (2006).
Phasing RNA polymerase II using intrinsically bound Zn atoms: an updated structural model.
  Structure, 14, 973-982.
PDB code: 2b8k
16496021 P.Aloy, and R.B.Russell (2006).
Structural systems biology: modelling protein interactions.
  Nat Rev Mol Cell Biol, 7, 188-197.  
17146456 P.Cramer (2006).
Deciphering the RNA polymerase II structure: a personal perspective.
  Nat Struct Mol Biol, 13, 1042-1044.  
16549500 P.Percipalle, and N.Visa (2006).
Molecular functions of nuclear actin in transcription.
  J Cell Biol, 172, 967-971.  
17147473 P.S.Salgado, M.R.Koivunen, E.V.Makeyev, D.H.Bamford, D.I.Stuart, and J.M.Grimes (2006).
The structure of an RNAi polymerase links RNA silencing and transcription.
  PLoS Biol, 4, e434.
PDB codes: 2j7n 2j7o
16651655 R.Das, K.Dufu, B.Romney, M.Feldt, M.Elenko, and R.Reed (2006).
Functional coupling of RNAP II transcription to spliceosome assembly.
  Genes Dev, 20, 1100-1109.  
17174884 R.Landick, and R.Kornberg (2006).
A long time in the making--the Nobel Prize for RNA polymerase.
  Cell, 127, 1087-1090.  
17098194 S.A.Kostek, P.Grob, S.De Carlo, J.S.Lipscomb, F.Garczarek, and E.Nogales (2006).
Molecular architecture and conformational flexibility of human RNA polymerase II.
  Structure, 14, 1691-1700.  
16525731 S.H.An, J.Y.Shang, Y.H.Liu, V.S.Kumar, Z.J.Guo, D.Wang, Z.N.Yang, and C.X.Zhang (2006).
Characterization of a unique gene ORF135 from Helicoverpa armigera single nucleocapsid nucleopolyhedrovirus.
  Virus Genes, 32, 21-26.  
17030604 S.Li, B.Ding, R.Chen, C.Ruggiero, and X.Chen (2006).
Evidence that the transcription elongation function of Rpb9 is involved in transcription-coupled DNA repair in Saccharomyces cerevisiae.
  Mol Cell Biol, 26, 9430-9441.  
16900098 T.A.Steitz (2006).
Visualizing polynucleotide polymerase machines at work.
  EMBO J, 25, 3458-3468.  
17069655 T.J.Goodwin, M.I.Butler, and R.T.Poulter (2006).
Multiple, non-allelic, intein-coding sequences in eukaryotic RNA polymerase genes.
  BMC Biol, 4, 38.  
16431989 T.Lenasi, B.M.Peterlin, and P.Dovc (2006).
Distal regulation of alternative splicing by splicing enhancer in equine beta-casein intron 1.
  RNA, 12, 498-507.  
16537373 V.R.Tadigotla, D.O Maoiléidigh, A.M.Sengupta, V.Epshtein, R.H.Ebright, E.Nudler, and A.E.Ruckenstein (2006).
Thermodynamic and kinetic modeling of transcriptional pausing.
  Proc Natl Acad Sci U S A, 103, 4439-4444.  
16524917 V.Trinh, M.F.Langelier, J.Archambault, and B.Coulombe (2006).
Structural perspective on mutations affecting the function of multisubunit RNA polymerases.
  Microbiol Mol Biol Rev, 70, 12-36.  
16769904 X.Hu, S.Malik, C.C.Negroiu, K.Hubbard, C.N.Velalar, B.Hampton, D.Grosu, J.Catalano, R.G.Roeder, and A.Gnatt (2006).
A Mediator-responsive form of metazoan RNA polymerase II.
  Proc Natl Acad Sci U S A, 103, 9506-9511.  
16094453 B.Coulombe, and M.F.Langelier (2005).
Functional dissection of the catalytic mechanism of mammalian RNA polymerase II.
  Biochem Cell Biol, 83, 497-504.  
15612920 C.Zaros, and P.Thuriaux (2005).
Rpc25, a conserved RNA polymerase III subunit, is critical for transcription initiation.
  Mol Microbiol, 55, 104-114.  
15831464 C.Zhang, K.L.Zobeck, and Z.F.Burton (2005).
Human RNA polymerase II elongation in slow motion: role of the TFIIF RAP74 alpha1 helix in nucleoside triphosphate-driven translocation.
  Mol Cell Biol, 25, 3583-3595.  
16140984 D.Pontier, G.Yahubyan, D.Vega, A.Bulski, J.Saez-Vasquez, M.A.Hakimi, S.Lerbs-Mache, V.Colot, and T.Lagrange (2005).
Reinforcement of silencing at transposons and highly repeated sequences requires the concerted action of two distinct RNA polymerases IV in Arabidopsis.
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16167380 D.Temiakov, N.Zenkin, M.N.Vassylyeva, A.Perederina, T.H.Tahirov, E.Kashkina, M.Savkina, S.Zorov, V.Nikiforov, N.Igarashi, N.Matsugaki, S.Wakatsuki, K.Severinov, and D.G.Vassylyev (2005).
Structural basis of transcription inhibition by antibiotic streptolydigin.
  Mol Cell, 19, 655-666.
PDB code: 2a6h
16135821 F.Werner, and R.O.Weinzierl (2005).
Direct modulation of RNA polymerase core functions by basal transcription factors.
  Mol Cell Biol, 25, 8344-8355.  
15680325 G.Bar-Nahum, V.Epshtein, A.E.Ruckenstein, R.Rafikov, A.Mustaev, and E.Nudler (2005).
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16282592 H.Meka, F.Werner, S.C.Cordell, S.Onesti, and P.Brick (2005).
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PDB code: 2c35
16096056 I.Artsimovitch, M.N.Vassylyeva, D.Svetlov, V.Svetlov, A.Perederina, N.Igarashi, N.Matsugaki, S.Wakatsuki, T.H.Tahirov, and D.G.Vassylyev (2005).
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PDB codes: 2a68 2a69 2a6e
15542547 J.L.Knight, V.Mekler, J.Mukhopadhyay, R.H.Ebright, and R.M.Levy (2005).
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15743411 K.Hayashi, T.Watanabe, A.Tanaka, T.Furumoto, C.Sato-Tsuchiya, M.Kimura, M.Yokoi, A.Ishihama, F.Hanaoka, and Y.Ohkuma (2005).
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16147988 M.A.Freire-Picos, S.Krishnamurthy, Z.W.Sun, and M.Hampsey (2005).
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15886393 M.F.Langelier, D.Baali, V.Trinh, J.Greenblatt, J.Archambault, and B.Coulombe (2005).
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16214896 M.Palangat, D.B.Renner, D.H.Price, and R.Landick (2005).
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16285916 R.A.Mooney, S.A.Darst, and R.Landick (2005).
Sigma and RNA polymerase: an on-again, off-again relationship?
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15840809 R.J.Grainger, and J.D.Beggs (2005).
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15714199 S.J.Greive, and P.H.von Hippel (2005).
Thinking quantitatively about transcriptional regulation.
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15574517 S.O.Gudima, J.Chang, and J.M.Taylor (2005).
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16122422 S.Tuske, S.G.Sarafianos, X.Wang, B.Hudson, E.Sineva, J.Mukhopadhyay, J.J.Birktoft, O.Leroy, S.Ismail, A.D.Clark, C.Dharia, A.Napoli, O.Laptenko, J.Lee, S.Borukhov, R.H.Ebright, and E.Arnold (2005).
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PDB codes: 1zyr 2cw0
15987790 W.J.Benga, S.Grandemange, G.V.Shpakovski, E.K.Shematorova, C.Kedinger, and M.Vigneron (2005).
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15766525 Y.Onodera, J.R.Haag, T.Ream, P.C.Nunes, O.Pontes, and C.S.Pikaard (2005).
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PDB code: 1s0v
15523475 F.J.Asturias (2004).
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15610738 H.Kettenberger, K.J.Armache, and P.Cramer (2004).
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PDB codes: 1y1v 1y1w 1y1y 1y77
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PDB codes: 1smy 1t0x
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PDB codes: 1r9s 1r9t 1twa 1twc 1twf 1twg 1twh
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PDB code: 1nik
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Phasing the 30S ribosomal subunit structure.
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PDB code: 1pqv
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PDB code: 1nt9
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PDB codes: 1v33 1v34
12914698 N.Opalka, M.Chlenov, P.Chacon, W.J.Rice, W.Wriggers, and S.A.Darst (2003).
Structure and function of the transcription elongation factor GreB bound to bacterial RNA polymerase.
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12824381 P.Puntervoll, R.Linding, C.Gemünd, S.Chabanis-Davidson, M.Mattingsdal, S.Cameron, D.M.Martin, G.Ausiello, B.Brannetti, A.Costantini, F.Ferrè, V.Maselli, A.Via, G.Cesareni, F.Diella, G.Superti-Furga, L.Wyrwicz, C.Ramu, C.McGuigan, R.Gudavalli, I.Letunic, P.Bork, L.Rychlewski, B.Küster, M.Helmer-Citterich, W.N.Hunter, R.Aasland, and T.J.Gibson (2003).
ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins.
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12938174 P.Tompa (2003).
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12914690 R.C.Conaway, S.E.Kong, and J.W.Conaway (2003).
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Old dogs and new tricks: meeting on mechanisms of eukaryotic transcription.
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PDB code: 1kft
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Rpa12p, a conserved RNA polymerase I subunit with two functional domains.
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Deriving folds of macromolecular complexes through electron cryomicroscopy and bioinformatics approaches.
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12052871 Y.K.Kim, C.F.Bourgeois, C.Isel, M.J.Churcher, and J.Karn (2002).
Phosphorylation of the RNA polymerase II carboxyl-terminal domain by CDK9 is directly responsible for human immunodeficiency virus type 1 Tat-activated transcriptional elongation.
  Mol Cell Biol, 22, 4622-4637.  
11585929 D.P.Tran, S.J.Kim, N.J.Park, T.M.Jew, and H.G.Martinson (2001).
Mechanism of poly(A) signal transduction to RNA polymerase II in vitro.
  Mol Cell Biol, 21, 7495-7508.  
11741548 F.Todone, P.Brick, F.Werner, R.O.Weinzierl, and S.Onesti (2001).
Structure of an archaeal homolog of the eukaryotic RNA polymerase II RPB4/RPB7 complex.
  Mol Cell, 8, 1137-1143.
PDB code: 1go3
11486042 J.F.Briand, F.Navarro, P.Rematier, C.Boschiero, S.Labarre, M.Werner, G.V.Shpakovski, and P.Thuriaux (2001).
Partners of Rpb8p, a small subunit shared by yeast RNA polymerases I, II and III.
  Mol Cell Biol, 21, 6056-6065.  
11592390 R.D.Kornberg (2001).
The eukaryotic gene transcription machinery.
  Biol Chem, 382, 1103-1107.  
  11747469 S.Grandemange, S.Schaller, S.Yamano, S.Du Manoir, G.V.Shpakovski, M.G.Mattei, C.Kedinger, and M.Vigneron (2001).
A human RNA polymerase II subunit is encoded by a recently generated multigene family.
  BMC Mol Biol, 2, 14.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.