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Transcription PDB id
1i50
Jmol
Contents
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. *
Metals
_MN
_ZN ×8
Waters ×78
* Residue conservation analysis
PDB id:
1i50
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)
Resolution:
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
Date:
23-Feb-01     Release date:   23-Apr-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

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

 Enzyme reactions 
   Enzyme class: Chains A, B: E.C.2.7.7.6  - 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     RNA polymerase complex   9 terms 
  Biological process     response to DNA damage stimulus   10 terms 
  Biochemical function     protein binding     11 terms  

 

 
    reference    
 
 
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.
 
  ABSTRACT  
 
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 the author.  

Literature references that cite this PDB file's key reference

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Iwr1 directs RNA polymerase II nuclear import.
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Macromolecular assemblages.
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Architecture of the RNA polymerase-Spt4/5 complex and basis of universal transcription processivity.
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PDB code: 3qqc
21233849 F.Werner, and D.Grohmann (2011).
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21487437 J.N.Kuehner, E.L.Pearson, and C.Moore (2011).
Unravelling the means to an end: RNA polymerase II transcription termination.
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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.
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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).
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Archaeal RNA polymerase: the influence of the protruding stalk in crystal packing and preliminary biophysical analysis of the Rpo13 subunit.
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PDB code: 2y0s
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PDB codes: 2xub 2xv4
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The transcription inhibitor lipiarmycin blocks DNA fitting into the RNA polymerase catalytic site.
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X-ray structure and mechanism of RNA polymerase II stalled at an antineoplastic monofunctional platinum-DNA adduct.
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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.
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20360047 G.Ruprich-Robert, and P.Thuriaux (2010).
Non-canonical DNA transcription enzymes and the conservation of two-barrel RNA polymerases.
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20088966 H.Koyama, T.Ueda, T.Ito, and K.Sekimizu (2010).
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20418102 M.J.Muñoz, M.de la Mata, and A.R.Kornblihtt (2010).
The carboxy terminal domain of RNA polymerase II and alternative splicing.
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Nuclear functions of actin.
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21034443 R.O.Weinzierl (2010).
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20040576 S.Grünberg, C.Reich, M.E.Zeller, M.S.Bartlett, and M.Thomm (2010).
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21124318 S.Tagami, S.Sekine, T.Kumarevel, N.Hino, Y.Murayama, S.Kamegamori, M.Yamamoto, K.Sakamoto, and S.Yokoyama (2010).
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PDB codes: 3aoh 3aoi
19923176 S.Y.Hong, and P.J.Chen (2010).
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20483995 T.J.Gries, W.S.Kontur, M.W.Capp, R.M.Saecker, and M.T.Record (2010).
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19895816 W.J.Lane, and S.A.Darst (2010).
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Architecture of the RNA polymerase II-TFIIF complex revealed by cross-linking and mass spectrometry.
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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).
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E pluribus tres: the 2009 nobel prize in chemistry.
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Rpb9 subunit controls transcription fidelity by delaying NTP sequestration in RNA polymerase II.
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19109435 C.Y.Chen, C.C.Chang, C.F.Yen, M.T.Chiu, and W.H.Chang (2009).
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RNA polymerase II-TFIIB structure and mechanism of transcription initiation.
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PDB code: 3k1f
19489723 E.Nudler (2009).
RNA polymerase active center: the molecular engine of transcription.
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A movie of the RNA polymerase nucleotide addition cycle.
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Structure-function studies of the RNA polymerase II elongation complex.
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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.
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Structures of RNA polymerase-antibiotic complexes.
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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.
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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.
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PDB code: 3fki
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Structural biology: New beginnings for transcription.
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Sigma factors for cyanobacterial transcription.
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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.
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Conformational changes associated with template commitment in ATP-dependent chromatin remodeling by ISW2.
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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).
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Evolution of Complex RNA Polymerases: The Complete Archaeal RNA Polymerase Structure.
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PDB codes: 2waq 2wb1
19915655 A.Bashan, and A.Yonath (2008).
The linkage between ribosomal crystallography, metal ions, heteropolytungstates and functional flexibility.
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Transcription processing at 1,N2-ethenoguanine by human RNA polymerase II and bacteriophage T7 RNA polymerase.
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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.
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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.
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18235446 A.Hirata, B.J.Klein, and K.S.Murakami (2008).
The X-ray crystal structure of RNA polymerase from Archaea.
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PDB codes: 2pa8 2pmz 3hkz
18974734 A.J.Heck (2008).
Native mass spectrometry: a bridge between interactomics and structural biology.
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18849988 A.Muschielok, J.Andrecka, A.Jawhari, F.Brückner, P.Cramer, and J.Michaelis (2008).
A nano-positioning system for macromolecular structural analysis.
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18264749 B.A.Knutson, and S.S.Broyles (2008).
Expansion of poxvirus RNA polymerase subunits sharing homology with corresponding subunits of RNA polymerase II.
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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.
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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, V.de 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: