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PDBsum entry 1l9u

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protein metals Protein-protein interface(s) links
Transcription PDB id
1l9u
Jmol
Contents
Protein chains
224 a.a. *
1084 a.a. *
1183 a.a. *
92 a.a. *
322 a.a. *
Metals
_ZN ×4
_MG ×2
* Residue conservation analysis
PDB id:
1l9u
Name: Transcription
Title: Thermus aquaticus RNA polymerase holoenzyme at 4 a resolution
Structure: RNA polymerase, alpha subunit. Chain: a, b, j, k. RNA polymerase, beta subunit. Chain: c, l. RNA polymerase, beta-prime subunit. Chain: d, m. RNA polymerase, omega subunit. Chain: e, n. Sigma factor siga.
Source: Thermus aquaticus. Organism_taxid: 271. Gene: rpod. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Hexamer (from PQS)
Resolution:
4.00Å     R-factor:   not given    
Authors: K.S.Murakami,S.Masuda,S.A.Darst
Key ref:
K.S.Murakami et al. (2002). Structural basis of transcription initiation: RNA polymerase holoenzyme at 4 A resolution. Science, 296, 1280-1284. PubMed id: 12016306 DOI: 10.1126/science.1069594
Date:
26-Mar-02     Release date:   22-May-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q9KWU8  (RPOA_THEAQ) -  DNA-directed RNA polymerase subunit alpha
Seq:
Struc:
314 a.a.
224 a.a.
Protein chains
Pfam   ArchSchema ?
Q9KWU7  (RPOB_THEAQ) -  DNA-directed RNA polymerase subunit beta
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1119 a.a.
1084 a.a.
Protein chains
Pfam   ArchSchema ?
Q9KWU6  (RPOC_THEAQ) -  DNA-directed RNA polymerase subunit beta'
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1524 a.a.
1183 a.a.
Protein chains
Pfam   ArchSchema ?
Q9EVV4  (RPOZ_THEAQ) -  DNA-directed RNA polymerase subunit omega
Seq:
Struc:
99 a.a.
92 a.a.
Protein chains
Pfam   ArchSchema ?
Q9EZJ8  (Q9EZJ8_THEAQ) -  RNA polymerase sigma factor SigA
Seq:
Struc:
438 a.a.
322 a.a.
Key:    PfamA domain  Secondary structure

 Enzyme reactions 
   Enzyme class: Chains A, B, C, D, E, J, K, L, M, N: 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!
  Biological process     DNA repair   4 terms 
  Biochemical function     transferase activity     8 terms  

 

 
    reference    
 
 
DOI no: 10.1126/science.1069594 Science 296:1280-1284 (2002)
PubMed id: 12016306  
 
 
Structural basis of transcription initiation: RNA polymerase holoenzyme at 4 A resolution.
K.S.Murakami, S.Masuda, S.A.Darst.
 
  ABSTRACT  
 
The crystal structure of the initiating form of Thermus aquaticus RNA polymerase, containing core RNA polymerase (alpha2betabeta'omega) and the promoter specificity sigma subunit, has been determined at 4 angstrom resolution. Important structural features of the RNA polymerase and their roles in positioning sigma within the initiation complex are delineated, as well as the role played by sigma in modulating the opening of the RNA polymerase active-site channel. The two carboxyl-terminal domains of sigma are separated by 45 angstroms on the surface of the RNA polymerase, but are linked by an extended loop. The loop winds near the RNA polymerase active site, where it may play a role in initiating nucleotide substrate binding, and out through the RNA exit channel. The advancing RNA transcript must displace the loop, leading to abortive initiation and ultimately to sigma release.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. Taq RNAP holoenzyme structure. Views of the Taq RNAP holoenzyme structure, shown as a molecular surface but with important features of core RNAP shown as -carbon backbone worms without the corresponding surfaces (color coding of surfaces and worms is indicated). The molecular surface of is transparent, allowing the orange -carbon backbone worm to be seen as well. (A) The same view as in Fig. 1A. The Zn2+ ion bound in the 'ZBD is shown as a light-green sphere. Surfaces of corresponding to residues important for promoter recognition and melting are color coded as follows: melting/ 10 element nontemplate strand binding, yellow; 10 element recognition, green; extended 10 element recognition, blue; 35 element recognition, brown. (B) Partial, magnified view, obtained from (A) by rotation about the horizontal axis as indicated. Obscuring portions of have been removed to reveal the inside of the main channel. The outline of is shown as a cyan line. The active-site Mg2+ is shown as a magenta sphere. The disordered segment of is denoted by orange dots, connecting residues 336 to 346, which are labeled. The NH[2]-terminus of the fragment (corresponding to Taq A residue 93), which points into the RNAP channel toward the active-site Mg2+, is indicated (N). The figure was made with the program GRASP (41).
Figure 4.
Fig. 4. Electrostatic distribution of holoenzyme and region 1.1. (A) Two surface views of the RNAP holoenzyme, color coded according to electrostatic surface potential (negative, red; neutral, white; positive, blue). The transparent -carbon backbone worm of (orange) is superimposed. (Left) Same view as in Fig. 1A. (Right) View obtained from the left view by a rotation about the vertical axis as indicated; the active-site Mg2+ in the back of the main RNAP channel is visible as a magenta sphere. The NH[2]-terminus of the fragment (corresponding to Taq A residue 93), which points into the RNAP channel toward the active-site Mg2+, is indicated (N). (B) Schematic diagram illustrating the proposed mechanism of the negatively charged region 1.1 in promoting open complex formation. The viewing angle is similar to that in Fig. 1A. Two states of the RNAP holoenzyme-promoter DNA complex are illustrated. The positioning of the DNA is according to (35). The core RNAP is colored gray, and is colored orange, except region 1.1, which is colored magenta. (Left) The initial closed promoter complex (RP[c]), where we propose that region 1.1 is positioned inside the positively charged RNAP channel [protecting it from hydroxyl-radical cleavage (34)], holding the channel open (indicated by thick black lines) to allow entry of double-stranded DNA. (Right) Final open promoter complex (RP[o]), where DNA has entered the RNAP main channel and the channel has closed, ejecting region 1.1, where it is exposed in solution to proteases (35) and hydroxyl-radical cleavage (34). (A) was made with the program GRASP (41).
 
  The above figures are reprinted by permission from the AAAs: Science (2002, 296, 1280-1284) copyright 2002.  
  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
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
20935043 H.Y.Yeh, T.C.Chen, K.M.Liou, H.T.Hsu, K.M.Chung, L.L.Hsu, and B.Y.Chang (2011).
The core-independent promoter-specific interaction of primary sigma factor.
  Nucleic Acids Res, 39, 913-925.  
21414325 J.Trepreau, E.Girard, A.P.Maillard, E.de Rosny, I.Petit-Haertlein, R.Kahn, and J.Covès (2011).
Structural Basis for Metal Sensing by CnrX.
  J Mol Biol, 408, 766-779.
PDB codes: 2y39 2y3b 2y3d 2y3g 2y3h
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.  
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.  
20133868 B.Cámara, M.Liu, J.Reynolds, A.Shadrin, B.Liu, K.Kwok, P.Simpson, R.Weinzierl, K.Severinov, E.Cota, S.Matthews, and S.R.Wigneshweraraj (2010).
T7 phage protein Gp2 inhibits the Escherichia coli RNA polymerase by antagonizing stable DNA strand separation near the transcription start site.
  Proc Natl Acad Sci U S A, 107, 2247-2252.
PDB code: 2wnm
  21029433 D.M.Hinton (2010).
Transcriptional control in the prereplicative phase of T4 development.
  Virol J, 7, 289.  
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.  
  21029432 E.P.Geiduschek, and G.A.Kassavetis (2010).
Transcription of the T4 late genes.
  Virol J, 7, 288.  
20615963 J.Chen, S.A.Darst, and D.Thirumalai (2010).
Promoter melting triggered by bacterial RNA polymerase occurs in three steps.
  Proc Natl Acad Sci U S A, 107, 12523-12528.  
20735776 J.Herrou, R.Foreman, A.Fiebig, and S.Crosson (2010).
A structural model of anti-anti-σ inhibition by a two-component receiver domain: the PhyR stress response regulator.
  Mol Microbiol, 78, 290-304.
PDB code: 3n0r
20184899 K.G.Thakur, T.Praveena, and B.Gopal (2010).
Structural and biochemical bases for the redox sensitivity of Mycobacterium tuberculosis RslA.
  J Mol Biol, 397, 1199-1208.
PDB code: 3hug
20702425 L.F.Westblade, E.A.Campbell, C.Pukhrambam, J.C.Padovan, B.E.Nickels, V.Lamour, and S.A.Darst (2010).
Structural basis for the bacterial transcription-repair coupling factor/RNA polymerase interaction.
  Nucleic Acids Res, 38, 8357-8369.
PDB code: 3mlq
20606072 M.K.Taha, S.T.Hedberg, M.Szatanik, E.Hong, C.Ruckly, R.Abad, S.Bertrand, F.Carion, H.Claus, A.Corso, R.Enríquez, S.Heuberger, W.Hryniewicz, K.A.Jolley, P.Kriz, M.Mollerach, M.Musilek, A.Neri, P.Olcén, M.Pana, A.Skoczynska, C.Sorhouet Pereira, P.Stefanelli, G.Tzanakaki, M.Unemo, J.A.Vázquez, U.Vogel, and I.Wasko (2010).
Multicenter study for defining the breakpoint for rifampin resistance in Neisseria meningitidis by rpoB sequencing.
  Antimicrob Agents Chemother, 54, 3651-3658.  
  20856905 N.Opalka, J.Brown, W.J.Lane, K.A.Twist, R.Landick, F.J.Asturias, and S.A.Darst (2010).
Complete structural model of Escherichia coli RNA polymerase from a hybrid approach.
  PLoS Biol, 8, 0.
PDB codes: 3lti 3lu0
20070531 P.G.Devi, E.A.Campbell, S.A.Darst, and B.E.Nickels (2010).
Utilization of variably spaced promoter-like elements by the bacterial RNA polymerase holoenzyme during early elongation.
  Mol Microbiol, 75, 607-622.  
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
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.  
19895816 W.J.Lane, and S.A.Darst (2010).
Molecular evolution of multisubunit RNA polymerases: structural analysis.
  J Mol Biol, 395, 686-704.  
19965383 X.Liu, D.A.Bushnell, D.Wang, G.Calero, and R.D.Kornberg (2010).
Structure of an RNA polymerase II-TFIIB complex and the transcription initiation mechanism.
  Science, 327, 206-209.
PDB code: 3k7a
20534498 Y.Yuzenkova, and N.Zenkin (2010).
Central role of the RNA polymerase trigger loop in intrinsic RNA hydrolysis.
  Proc Natl Acad Sci U S A, 107, 10878-10883.  
19538447 A.D.Klocko, and K.M.Wassarman (2009).
6S RNA binding to Esigma(70) requires a positively charged surface of sigma(70) region 4.2.
  Mol Microbiol, 73, 152-164.  
19880312 A.Hirata, and K.S.Murakami (2009).
Archaeal RNA polymerase.
  Curr Opin Struct Biol, 19, 724-731.  
19257840 A.Tupin, M.Gualtieri, K.Brodolin, and J.P.Leonetti (2009).
Myxopyronin: a punch in the jaws of bacterial RNA polymerase.
  Future Microbiol, 4, 145-149.  
19400790 B.M.Koo, V.A.Rhodius, E.A.Campbell, and C.A.Gross (2009).
Mutational analysis of Escherichia coli sigma28 and its target promoters reveals recognition of a composite -10 region, comprised of an 'extended -10' motif and a core -10 element.
  Mol Microbiol, 72, 830-843.  
19400791 B.M.Koo, V.A.Rhodius, E.A.Campbell, and C.A.Gross (2009).
Dissection of recognition determinants of Escherichia coli sigma32 suggests a composite -10 region with an 'extended -10' motif and a core -10 element.
  Mol Microbiol, 72, 815-829.  
19596241 C.L.Stallings, N.C.Stephanou, L.Chu, A.Hochschild, B.E.Nickels, and M.S.Glickman (2009).
CarD is an essential regulator of rRNA transcription required for Mycobacterium tuberculosis persistence.
  Cell, 138, 146-159.  
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
19735077 E.B.Johnston, P.J.Lewis, and R.Griffith (2009).
The interaction of Bacillus subtilis sigmaA with RNA polymerase.
  Protein Sci, 18, 2287-2297.  
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
19139410 I.G.Hook-Barnard, and D.M.Hinton (2009).
The promoter spacer influences transcription initiation via {sigma}70 region 1.1 of Escherichia coli RNA polymerase.
  Proc Natl Acad Sci U S A, 106, 737-742.  
18976666 L.A.Schroeder, T.J.Gries, R.M.Saecker, M.T.Record, M.E.Harris, and P.L.DeHaseth (2009).
Evidence for a tyrosine-adenine stacking interaction and for a short-lived open intermediate subsequent to initial binding of Escherichia coli RNA polymerase to promoter DNA.
  J Mol Biol, 385, 339-349.  
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.  
19111618 N.R.Gassman, S.O.Ho, Y.Korlann, J.Chiang, Y.Wu, L.J.Perry, Y.Kim, and S.Weiss (2009).
In vivo assembly and single-molecule characterization of the transcription machinery from Shewanella oneidensis MR-1.
  Protein Expr Purif, 65, 66-76.  
19441027 P.Yan, T.Wang, G.J.Newton, T.V.Knyushko, Y.Xiong, D.J.Bigelow, T.C.Squier, and M.U.Mayer (2009).
A targeted releasable affinity probe (TRAP) for in vivo photocrosslinking.
  Chembiochem, 10, 1507-1518.  
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.  
19965468 S.Kühner, V.van Noort, M.J.Betts, A.Leo-Macias, C.Batisse, M.Rode, T.Yamada, T.Maier, S.Bader, P.Beltran-Alvarez, D.Castaño-Diez, W.H.Chen, D.Devos, M.Güell, T.Norambuena, I.Racke, V.Rybin, A.Schmidt, E.Yus, R.Aebersold, R.Herrmann, B.Böttcher, A.S.Frangakis, R.B.Russell, L.Serrano, P.Bork, and A.C.Gavin (2009).
Proteome organization in a genome-reduced bacterium.
  Science, 326, 1235-1240.  
19354299 S.M.Cheal, M.Ng, B.Barrios, Z.Miao, A.K.Kalani, and C.F.Meares (2009).
Mapping protein-protein interactions by localized oxidation: consequences of the reach of hydroxyl radical.
  Biochemistry, 48, 4577-4586.  
18826409 A.H.Yuan, B.D.Gregory, J.S.Sharp, K.D.McCleary, S.L.Dove, and A.Hochschild (2008).
Rsd family proteins make simultaneous interactions with regions 2 and 4 of the primary sigma factor.
  Mol Microbiol, 70, 1136-1151.  
18333883 A.Hatoum, and J.Roberts (2008).
Prevalence of RNA polymerase stalling at Escherichia coli promoters after open complex formation.
  Mol Microbiol, 68, 17-28.  
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
18641146 A.Kanda, K.Tsuneishi, A.Mori, K.Ohnishi, A.Kiba, and Y.Hikichi (2008).
An amino acid substitution at position 740 in sigma70 of Ralstonia solanacearum strain OE1-1 affects its in planta growth.
  Appl Environ Microbiol, 74, 5841-5844.  
18296515 A.Kumar, and C.P.Moran (2008).
Promoter activation by repositioning of RNA polymerase.
  J Bacteriol, 190, 3110-3117.  
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
18272182 C.E.Vrentas, T.Gaal, M.B.Berkmen, S.T.Rutherford, S.P.Haugen, D.G.Vassylyev, W.Ross, and R.L.Gourse (2008).
Still looking for the magic spot: the crystallographically defined binding site for ppGpp on RNA polymerase is unlikely to be responsible for rRNA transcription regulation.
  J Mol Biol, 377, 551-564.  
18995832 D.Bose, T.Pape, P.C.Burrows, M.Rappas, S.R.Wigneshweraraj, M.Buck, and X.Zhang (2008).
Organization of an activator-bound RNA polymerase holoenzyme.
  Mol Cell, 32, 337-346.  
18375176 E.A.Campbell, L.F.Westblade, and S.A.Darst (2008).
Regulation of bacterial RNA polymerase sigma factor activity: a structural perspective.
  Curr Opin Microbiol, 11, 121-127.  
18940669 E.C.Schwartz, A.Shekhtman, K.Dutta, M.R.Pratt, D.Cowburn, S.Darst, and T.W.Muir (2008).
A full-length group 1 bacterial sigma factor adopts a compact structure incompatible with DNA binding.
  Chem Biol, 15, 1091-1103.
PDB code: 2k6x
18190515 F.Cava, M.A.de Pedro, E.Blas-Galindo, G.S.Waldo, L.F.Westblade, and J.Berenguer (2008).
Expression and use of superfolder green fluorescent protein at high temperatures in vivo: a tool to study extreme thermophile biology.
  Environ Microbiol, 10, 605-613.  
18468900 F.Werner (2008).
Structural evolution of multisubunit RNA polymerases.
  Trends Microbiol, 16, 247-250.  
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
18948533 K.J.Durniak, S.Bailey, and T.A.Steitz (2008).
The structure of a transcribing T7 RNA polymerase in transition from initiation to elongation.
  Science, 322, 553-557.
PDB codes: 3e2e 3e3j
18411280 K.Tran, and J.D.Gralla (2008).
Control of the timing of promoter escape and RNA catalysis by the transcription factor IIb fingertip.
  J Biol Chem, 283, 15665-15671.  
18281386 M.Djordjevic, and R.Bundschuh (2008).
Formation of the open complex by bacterial RNA polymerase--a quantitative model.
  Biophys J, 94, 4233-4248.  
19061645 M.L.Gleghorn, E.K.Davydova, L.B.Rothman-Denes, and K.S.Murakami (2008).
Structural basis for DNA-hairpin promoter recognition by the bacteriophage N4 virion RNA polymerase.
  Mol Cell, 32, 707-717.
PDB codes: 3c2p 3c3l 3c46
18281402 N.Barinova, E.Zhilina, I.Bass, V.Nikiforov, and A.Kulbachinskiy (2008).
Lineage-specific amino acid substitutions in region 2 of the RNA polymerase sigma subunit affect the temperature of promoter opening.
  J Bacteriol, 190, 3088-3092.  
18832144 P.Deighan, C.M.Diez, M.Leibman, A.Hochschild, and B.E.Nickels (2008).
The bacteriophage lambda Q antiterminator protein contacts the beta-flap domain of RNA polymerase.
  Proc Natl Acad Sci U S A, 105, 15305-15310.  
18818199 P.England, L.F.Westblade, G.Karimova, V.Robbe-Saule, F.Norel, and A.Kolb (2008).
Binding of the unorthodox transcription activator, Crl, to the components of the transcription machinery.
  J Biol Chem, 283, 33455-33464.  
18485078 R.P.Bonocora, G.Caignan, C.Woodrell, M.H.Werner, and D.M.Hinton (2008).
A basic/hydrophobic cleft of the T4 activator MotA interacts with the C-terminus of E.coli sigma70 to activate middle gene transcription.
  Mol Microbiol, 69, 331-343.  
18280161 S.Borukhov, and E.Nudler (2008).
RNA polymerase: the vehicle of transcription.
  Trends Microbiol, 16, 126-134.  
18287032 S.P.Haugen, W.Ross, M.Manrique, and R.L.Gourse (2008).
Fine structure of the promoter-sigma region 1.2 interaction.
  Proc Natl Acad Sci U S A, 105, 3292-3297.  
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.  
18331472 S.Wigneshweraraj, D.Bose, P.C.Burrows, N.Joly, J.Schumacher, M.Rappas, T.Pape, X.Zhang, P.Stockley, K.Severinov, and M.Buck (2008).
Modus operandi of the bacterial RNA polymerase containing the sigma54 promoter-specificity factor.
  Mol Microbiol, 68, 538-546.  
17763923 Y.Tutar (2008).
Chemical Linkage at Allosteric Activation of E. coli cAMP Receptor Protein.
  Protein J, 27, 21-29.  
18052851 B.T.Glaser, V.Bergendahl, N.E.Thompson, B.Olson, and R.R.Burgess (2007).
LRET-based HTS of a small-compound library for inhibitors of bacterial RNA polymerase.
  Assay Drug Dev Technol, 5, 759-768.  
17470797 C.A.Davis, C.A.Bingman, R.Landick, M.T.Record, and R.M.Saecker (2007).
Real-time footprinting of DNA in the first kinetically significant intermediate in open complex formation by Escherichia coli RNA polymerase.
  Proc Natl Acad Sci U S A, 104, 7833-7838.  
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.  
17803943 E.A.Campbell, R.Greenwell, J.R.Anthony, S.Wang, L.Lim, K.Das, H.J.Sofia, T.J.Donohue, and S.A.Darst (2007).
A conserved structural module regulates transcriptional responses to diverse stress signals in bacteria.
  Mol Cell, 27, 793-805.
PDB codes: 2q1z 2z2s
17356883 E.A.Lysenko (2007).
Plant sigma factors and their role in plastid transcription.
  Plant Cell Rep, 26, 845-859.  
17681541 G.A.Patikoglou, L.F.Westblade, E.A.Campbell, V.Lamour, W.J.Lane, and S.A.Darst (2007).
Crystal structure of the Escherichia coli regulator of sigma70, Rsd, in complex with sigma70 domain 4.
  J Mol Biol, 372, 649-659.
PDB code: 2p7v
  17329813 K.Okada, H.Ichihara, H.Takahashi, N.Fujita, A.Ishihama, and T.Hakoshima (2007).
Preparation and preliminary X-ray diffraction analysis of crystals of bacterial flagellar sigma factor sigma 28 in complex with the sigma 28-binding region of its antisigma factor, FlgM.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 196-199.  
17567604 L.A.Schroeder, A.J.Choi, and P.L.DeHaseth (2007).
The -11A of promoter DNA and two conserved amino acids in the melting region of sigma70 both directly affect the rate limiting step in formation of the stable RNA polymerase-promoter complex, but they do not necessarily interact.
  Nucleic Acids Res, 35, 4141-4153.  
17332752 M.Leibman, and A.Hochschild (2007).
A sigma-core interaction of the RNA polymerase holoenzyme that enhances promoter escape.
  EMBO J, 26, 1579-1590.  
17268549 N.Zenkin, A.Kulbachinskiy, Y.Yuzenkova, A.Mustaev, I.Bass, K.Severinov, and K.Brodolin (2007).
Region 1.2 of the RNA polymerase sigma subunit controls recognition of the -10 promoter element.
  EMBO J, 26, 955-964.  
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.  
17275836 T.J.Santangelo, L.Cubonová, C.L.James, and J.N.Reeve (2007).
TFB1 or TFB2 is sufficient for Thermococcus kodakaraensis viability and for basal transcription in vitro.
  J Mol Biol, 367, 344-357.  
17367295 Y.A.Khodak, O.N.Koroleva, and V.L.Drutsa (2007).
A system for heterologous expression and isolation of Escherichia coli RNA polymerase and its components.
  Biochemistry (Mosc), 72, 178-187.  
16798040 A.Feklistov, N.Barinova, A.Sevostyanova, E.Heyduk, I.Bass, I.Vvedenskaya, K.Kuznedelov, E.Merkiene, E.Stavrovskaya, S.Klimasauskas, V.Nikiforov, T.Heyduk, K.Severinov, and A.Kulbachinskiy (2006).
A basal promoter element recognized by free RNA polymerase sigma subunit determines promoter recognition by RNA polymerase holoenzyme.
  Mol Cell, 23, 97.  
16469698 A.M.Deaconescu, A.L.Chambers, A.J.Smith, B.E.Nickels, A.Hochschild, N.J.Savery, and S.A.Darst (2006).
Structural basis for bacterial transcription-coupled DNA repair.
  Cell, 124, 507-520.
PDB code: 2eyq
16420370 A.Typas, and R.Hengge (2006).
Role of the spacer between the -35 and -10 regions in sigmas promoter selectivity in Escherichia coli.
  Mol Microbiol, 59, 1037-1051.  
17081994 B.E.Nickels, C.W.Roberts, J.W.Roberts, and A.Hochschild (2006).
RNA-mediated destabilization of the sigma(70) region 4/beta flap interaction facilitates engagement of RNA polymerase by the Q antiterminator.
  Mol Cell, 24, 457-468.  
16452409 D.M.Hinton, S.Vuthoori, and R.Mulamba (2006).
The bacteriophage T4 inhibitor and coactivator AsiA inhibits Escherichia coli RNA Polymerase more rapidly in the absence of sigma70 region 1.1: evidence that region 1.1 stabilizes the interaction between sigma70 and core.
  J Bacteriol, 188, 1279-1285.  
16914440 E.Kashkina, M.Anikin, T.H.Tahirov, S.N.Kochetkov, D.G.Vassylyev, and D.Temiakov (2006).
Elongation complexes of Thermus thermophilus RNA polymerase that possess distinct translocation conformations.
  Nucleic Acids Res, 34, 4036-4045.  
17012380 I.Hook-Barnard, X.B.Johnson, and D.M.Hinton (2006).
Escherichia coli RNA polymerase recognition of a sigma70-dependent promoter requiring a -35 DNA element and an extended -10 TGn motif.
  J Bacteriol, 188, 8352-8359.  
  19669433 J.D.Bashford (2006).
Salerno's model of DNA re-analysed: could breather solitons have biological significance?
  J Biol Phys, 32, 27-47.  
16635801 J.J.Barker (2006).
Antibacterial drug discovery and structure-based design.
  Drug Discov Today, 11, 391-404.  
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.  
16996538 K.Baxter, J.Lee, L.Minakhin, K.Severinov, and D.M.Hinton (2006).
Mutational analysis of sigma70 region 4 needed for appropriation by the bacteriophage T4 transcription factors AsiA and MotA.
  J Mol Biol, 363, 931-944.  
16528104 M.A.Ramírez-Romero, I.Masulis, M.A.Cevallos, V.González, and G.Dávila (2006).
The Rhizobium etli sigma70 (SigA) factor recognizes a lax consensus promoter.
  Nucleic Acids Res, 34, 1470-1480.  
16484205 M.J.Wilson, and I.L.Lamont (2006).
Mutational analysis of an extracytoplasmic-function sigma factor to investigate its interactions with RNA polymerase and DNA.
  J Bacteriol, 188, 1935-1942.  
17075066 M.K.Sorenson, and S.A.Darst (2006).
Disulfide cross-linking indicates that FlgM-bound and free sigma28 adopt similar conformations.
  Proc Natl Acad Sci U S A, 103, 16722-16727.  
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.  
16815708 P.Deighan, and A.Hochschild (2006).
Conformational toggle triggers a modulator of RNA polymerase activity.
  Trends Biochem Sci, 31, 424-426.  
16718597 V.Braun, S.Mahren, and A.Sauter (2006).
Gene regulation by transmembrane signaling.
  Biometals, 19, 103-113.  
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.  
16475805 W.S.Kontur, R.M.Saecker, C.A.Davis, M.W.Capp, and M.T.Record (2006).
Solute probes of conformational changes in open complex (RPo) formation by Escherichia coli RNA polymerase at the lambdaPR promoter: evidence for unmasking of the active site in the isomerization step and for large-scale coupled folding in the subsequent conversion to RPo.
  Biochemistry, 45, 2161-2177.  
15687384 A.J.Smith, and N.J.Savery (2005).
RNA polymerase mutants defective in the initiation of transcription-coupled DNA repair.
  Nucleic Acids Res, 33, 755-764.  
16285917 A.N.Kapanidis, E.Margeat, T.A.Laurence, S.Doose, S.O.Ho, J.Mukhopadhyay, E.Kortkhonjia, V.Mekler, R.H.Ebright, and S.Weiss (2005).
Retention of transcription initiation factor sigma70 in transcription elongation: single-molecule analysis.
  Mol Cell, 20, 347-356.  
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.  
15761057 B.E.Nickels, S.J.Garrity, V.Mekler, L.Minakhin, K.Severinov, R.H.Ebright, and A.Hochschild (2005).
The interaction between sigma70 and the beta-flap of Escherichia coli RNA polymerase inhibits extension of nascent RNA during early elongation.
  Proc Natl Acad Sci U S A, 102, 4488-4493.  
15626761 C.A.Davis, M.W.Capp, M.T.Record, and R.M.Saecker (2005).
The effects of upstream DNA on open complex formation by Escherichia coli RNA polymerase.
  Proc Natl Acad Sci U S A, 102, 285-290.  
16204187 C.E.Vrentas, T.Gaal, W.Ross, R.H.Ebright, and R.L.Gourse (2005).
Response of RNA polymerase to ppGpp: requirement for the omega subunit and relief of this requirement by DksA.
  Genes Dev, 19, 2378-2387.  
15817381 D.M.Hinton (2005).
Molecular gymnastics: distortion of an RNA polymerase sigma factor.
  Trends Microbiol, 13, 140-143.  
15659674 H.Prince, R.Zhou, and L.Kroos (2005).
Substrate requirements for regulated intramembrane proteolysis of Bacillus subtilis pro-sigmaK.
  J Bacteriol, 187, 961-971.  
16045607 I.Barák, and A.J.Wilkinson (2005).
Where asymmetry in gene expression originates.
  Mol Microbiol, 57, 611-620.  
15542547 J.L.Knight, V.Mekler, J.Mukhopadhyay, R.H.Ebright, and R.M.Levy (2005).
Distance-restrained docking of rifampicin and rifamycin SV to RNA polymerase using systematic FRET measurements: developing benchmarks of model quality and reliability.
  Biophys J, 88, 925-938.  
15819620 M.Ouhammouch, G.E.Langham, W.Hausner, A.J.Simpson, N.M.El-Sayed, and E.P.Geiduschek (2005).
Promoter architecture and response to a positive regulator of archaeal transcription.
  Mol Microbiol, 56, 625-637.  
15989968 M.Pal, A.S.Ponticelli, and D.S.Luse (2005).
The role of the transcription bubble and TFIIB in promoter clearance by RNA polymerase II.
  Mol Cell, 19, 101-110.  
15790859 M.Rappas, J.Schumacher, F.Beuron, H.Niwa, P.Bordes, S.Wigneshweraraj, C.A.Keetch, C.V.Robinson, M.Buck, and X.Zhang (2005).
Structural insights into the activity of enhancer-binding proteins.
  Science, 307, 1972-1975.
PDB codes: 2bjv 2bjw
16285916 R.A.Mooney, S.A.Darst, and R.Landick (2005).
Sigma and RNA polymerase: an on-again, off-again relationship?
  Mol Cell, 20, 335-345.  
16193283 S.Mahren, H.Schnell, and V.Braun (2005).
Occurrence and regulation of the ferric citrate transport system in Escherichia coli B, Klebsiella pneumoniae, Enterobacter aerogenes, and Photorhabdus luminescens.
  Arch Microbiol, 184, 175-186.  
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).
Inhibition of bacterial RNA polymerase by streptolydigin: stabilization of a straight-bridge-helix active-center conformation.
  Cell, 122, 541-552.
PDB codes: 1zyr 2cw0
15943816 T.Łoziński, and K.L.Wierzchowski (2005).
Mg2+-modulated KMnO4 reactivity of thymines in the open transcription complex reflects variation in the negative electrostatic potential along the separated DNA strands. Footprinting of Escherichia coli RNA polymerase complex at the lambdaP(R) promoter revisited.
  FEBS J, 272, 2838-2853.  
16102597 V.Braun, and S.Mahren (2005).
Transmembrane transcriptional control (surface signalling) of the Escherichia coli Fec type.
  FEMS Microbiol Rev, 29, 673-684.  
16333751 V.Braun, S.Mahren, and A.Sauter (2005).
Gene regulation by transmembrane signaling.
  Biometals, 18, 507-517.  
15650048 Y.Berghöfer-Hochheimer, C.Z.Lu, and C.A.Gross (2005).
Altering the interaction between sigma70 and RNA polymerase generates complexes with distinct transcription-elongation properties.
  Proc Natl Acad Sci U S A, 102, 1157-1162.  
15606780 A.Kulbachinskiy, A.Feklistov, I.Krasheninnikov, A.Goldfarb, and V.Nikiforov (2004).
Aptamers to Escherichia coli core RNA polymerase that sense its interaction with rifampicin, sigma-subunit and GreB.
  Eur J Biochem, 271, 4921-4931.  
15070756 B.D.Gregory, B.E.Nickels, S.J.Garrity, E.Severinova, L.Minakhin, R.J.Urbauer, J.L.Urbauer, T.Heyduk, K.Severinov, and A.Hochschild (2004).
A regulator that inhibits transcription by targeting an intersubunit interaction of the RNA polymerase holoenzyme.
  Proc Natl Acad Sci U S A, 101, 4554-4559.  
15122345 B.E.Nickels, J.Mukhopadhyay, S.J.Garrity, R.H.Ebright, and A.Hochschild (2004).
The sigma 70 subunit of RNA polymerase mediates a promoter-proximal pause at the lac promoter.
  Nat Struct Mol Biol, 11, 544-550.  
15082791 B.S.Chen, and M.Hampsey (2004).
Functional interaction between TFIIB and the Rpb2 subunit of RNA polymerase II: implications for the mechanism of transcription initiation.
  Mol Cell Biol, 24, 3983-3991.  
15282305 C.Jeronimo, M.F.Langelier, M.Zeghouf, M.Cojocaru, D.Bergeron, D.Baali, D.Forget, S.Mnaimneh, A.P.Davierwala, J.Pootoolal, M.Chandy, V.Canadien, B.K.Beattie, D.P.Richards, J.L.Workman, T.R.Hughes, J.Greenblatt, and B.Coulombe (2004).
RPAP1, a novel human RNA polymerase II-associated protein affinity purified with recombinant wild-type and mutated polymerase subunits.
  Mol Cell Biol, 24, 7043-7058.  
15035009 D.F.Browning, and S.J.Busby (2004).
The regulation of bacterial transcription initiation.
  Nat Rev Microbiol, 2, 57-65.  
14729958 D.Forget, M.F.Langelier, C.Thérien, V.Trinh, and B.Coulombe (2004).
Photo-cross-linking of a purified preinitiation complex reveals central roles for the RNA polymerase II mobile clamp and TFIIE in initiation mechanisms.
  Mol Cell Biol, 24, 1122-1131.  
15545634 E.Guisbert, C.Herman, C.Z.Lu, and C.A.Gross (2004).
A chaperone network controls the heat shock response in E. coli.
  Genes Dev, 18, 2812-2821.  
15265034 E.Sarubbi, F.Monti, E.Corti, A.Miele, and E.Selva (2004).
Mode of action of the microbial metabolite GE23077, a novel potent and selective inhibitor of bacterial RNA polymerase.
  Eur J Biochem, 271, 3146-3154.  
15093825 F.J.Asturias (2004).
RNA polymerase II structure, and organization of the preinitiation complex.
  Curr Opin Struct Biol, 14, 121-129.  
15060039 H.H.Hsu, W.C.Huang, J.P.Chen, L.Y.Huang, C.F.Wu, and B.Y.Chang (2004).
Properties of Bacillus subtilis sigma A factors with region 1.1 and the conserved Arg-103 at the N terminus of region 1.2 deleted.
  J Bacteriol, 186, 2366-2375.  
15547256 J.Ma, and M.M.Howe (2004).
Binding of the C-terminal domain of the alpha subunit of RNA polymerase to the phage mu middle promoter.
  J Bacteriol, 186, 7858-7864.  
15276828 J.R.Anthony, J.D.Newman, and T.J.Donohue (2004).
Interactions between the Rhodobacter sphaeroides ECF sigma factor, sigma(E), and its anti-sigma factor, ChrR.
  J Mol Biol, 341, 345-360.  
15596728 J.T.Wade, and K.Struhl (2004).
Association of RNA polymerase with transcribed regions in Escherichia coli.
  Proc Natl Acad Sci U S A, 101, 17777-17782.  
15122346 K.Brodolin, N.Zenkin, A.Mustaev, D.Mamaeva, and H.Heumann (2004).
The sigma 70 subunit of RNA polymerase induces lacUV5 promoter-proximal pausing of transcription.
  Nat Struct Mol Biol, 11, 551-557.  
15372084 M.B.Schmid (2004).
Seeing is believing: the impact of structural genomics on antimicrobial drug discovery.
  Nat Rev Microbiol, 2, 739-746.  
15516558 M.Horikoshi, T.Yura, S.Tsuchimoto, Y.Fukumori, and M.Kanemori (2004).
Conserved region 2.1 of Escherichia coli heat shock transcription factor sigma32 is required for modulating both metabolic stability and transcriptional activity.
  J Bacteriol, 186, 7474-7480.  
15070729 N.Zenkin, and K.Severinov (2004).
The role of RNA polymerase sigma subunit in promoter-independent initiation of transcription.
  Proc Natl Acad Sci U S A, 101, 4396-4400.  
15196470 P.Cramer (2004).
RNA polymerase II structure: from core to functional complexes.
  Curr Opin Genet Dev, 14, 218-226.  
15114340 S.Hahn (2004).
Structure and mechanism of the RNA polymerase II transcription machinery.
  Nat Struct Mol Biol, 11, 394-403.  
14963488 S.Roy, H.M.Lim, M.Liu, and S.Adhya (2004).
Asynchronous basepair openings in transcription initiation: CRP enhances the rate-limiting step.
  EMBO J, 23, 869-875.  
15060133 S.Takahata, K.Kasahara, M.Kawaichi, and T.Kokubo (2004).
Autonomous function of the amino-terminal inhibitory domain of TAF1 in transcriptional regulation.
  Mol Cell Biol, 24, 3089-3099.  
15333692 W.V.Cannon, J.Schumacher, and M.Buck (2004).
Nucleotide-dependent interactions between a fork junction-RNA polymerase complex and an AAA+ transcriptional activator protein.
  Nucleic Acids Res, 32, 4596-4608.  
12912910 A.Stüdemann, M.Noirclerc-Savoye, E.Klauck, G.Becker, D.Schneider, and R.Hengge (2003).
Sequential recognition of two distinct sites in sigma(S) by the proteolytic targeting factor RssB and ClpX.
  EMBO J, 22, 4111-4120.  
12746498 D.A.Bushnell, and R.D.Kornberg (2003).
Complete, 12-subunit RNA polymerase II at 4.1-A resolution: implications for the initiation of transcription.
  Proc Natl Acad Sci U S A, 100, 6969-6973.
PDB code: 1nik
12949113 D.H.Wells, and S.R.Long (2003).
Mutations in rpoBC suppress the defects of a Sinorhizobium meliloti relA mutant.
  J Bacteriol, 185, 5602-5610.  
12782794 F.J.Asturias, and J.L.Craighead (2003).
RNA polymerase II at initiation.
  Proc Natl Acad Sci U S A, 100, 6893-6895.  
12700252 F.Narberhaus, and S.Balsiger (2003).
Structure-function studies of Escherichia coli RpoH (sigma32) by in vitro linker insertion mutagenesis.
  J Bacteriol, 185, 2731-2738.  
12670993 J.Gowrishankar, K.Yamamoto, P.R.Subbarayan, and A.Ishihama (2003).
In vitro properties of RpoS (sigma(S)) mutants of Escherichia coli with postulated N-terminal subregion 1.1 or C-terminal region 4 deleted.
  J Bacteriol, 185, 2673-2679.  
12746495 K.J.Armache, H.Kettenberger, and P.Cramer (2003).
Architecture of initiation-competent 12-subunit RNA polymerase II.
  Proc Natl Acad Sci U S A, 100, 6964-6968.
PDB code: 1nt9
12581657 K.S.Murakami, and S.A.Darst (2003).
Bacterial RNA polymerases: the wholo story.
  Curr Opin Struct Biol, 13, 31-39.  
12820881 M.F.Simeonov, R.J.Bieber Urbauer, J.M.Gilmore, K.Adelman, E.N.Brody, A.Niedziela-Majka, L.Minakhin, T.Heyduk, and J.L.Urbauer (2003).
Characterization of the interactions between the bacteriophage T4 AsiA protein and RNA polymerase.
  Biochemistry, 42, 7717-7726.  
12815340 M.Machius (2003).
Structural biology: a high-tech tool for biomedical research.
  Curr Opin Nephrol Hypertens, 12, 431-438.  
12540296 M.S.Paget, and J.D.Helmann (2003).
The sigma70 family of sigma factors.
  Genome Biol, 4, 203.  
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.
  Cell, 114, 335-345.  
12697831 Q.Tan, M.H.Prysak, and N.A.Woychik (2003).
Loss of the Rpb4/Rpb7 subcomplex in a mutant form of the Rpb6 subunit shared by RNA polymerases I, II, and III.
  Mol Cell Biol, 23, 3329-3338.  
12732296 S.Borukhov, and E.Nudler (2003).
RNA polymerase holoenzyme: structure, function and biological implications.
  Curr Opin Microbiol, 6, 93.  
12753182 S.L.Dove, S.A.Darst, and A.Hochschild (2003).
Region 4 of sigma as a target for transcription regulation.
  Mol Microbiol, 48, 863-874.  
12618442 S.Mahren, and V.Braun (2003).
The FecI extracytoplasmic-function sigma factor of Escherichia coli interacts with the beta' subunit of RNA polymerase.
  J Bacteriol, 185, 1796-1802.  
14527281 S.Nechaev, and K.Severinov (2003).
Bacteriophage-induced modifications of host RNA polymerase.
  Annu Rev Microbiol, 57, 301-322.  
12756229 T.J.Santangelo, R.A.Mooney, R.Landick, and J.W.Roberts (2003).
RNA polymerase mutations that impair conversion to a termination-resistant complex by Q antiterminator proteins.
  Genes Dev, 17, 1281-1292.  
14527287 T.M.Gruber, and C.A.Gross (2003).
Multiple sigma subunits and the partitioning of bacterial transcription space.
  Annu Rev Microbiol, 57, 441-466.  
12620834 V.Bergendahl, T.Heyduk, and R.R.Burgess (2003).
Luminescence resonance energy transfer-based high-throughput screening assay for inhibitors of essential protein-protein interactions in bacterial RNA polymerase.
  Appl Environ Microbiol, 69, 1492-1498.  
14580350 W.H.Chung, J.L.Craighead, W.H.Chang, C.Ezeokonkwo, A.Bareket-Samish, R.D.Kornberg, and F.J.Asturias (2003).
RNA polymerase II/TFIIF structure and conserved organization of the initiation complex.
  Mol Cell, 12, 1003-1013.  
12756230 W.Ross, D.A.Schneider, B.J.Paul, A.Mertens, and R.L.Gourse (2003).
An intersubunit contact stimulating transcription initiation by E coli RNA polymerase: interaction of the alpha C-terminal domain and sigma region 4.
  Genes Dev, 17, 1293-1307.  
12080337 L.M.Hsu (2002).
Open season on RNA polymerase.
  Nat Struct Biol, 9, 502-504.  
12377565 M.B.Schmid (2002).
Structural proteomics: the potential of high-throughput structure determination.
  Trends Microbiol, 10, S27-S31.  
12468233 P.Aloy, and R.B.Russell (2002).
The third dimension for protein interactions and complexes.
  Trends Biochem Sci, 27, 633-638.  
12457703 R.Hengge-Aronis (2002).
Stationary phase gene regulation: what makes an Escherichia coli promoter sigmaS-selective?
  Curr Opin Microbiol, 5, 591-595.  
12422209 T.H.Tahirov, D.Temiakov, M.Anikin, V.Patlan, W.T.McAllister, D.G.Vassylyev, and S.Yokoyama (2002).
Structure of a T7 RNA polymerase elongation complex at 2.9 A resolution.
  Nature, 420, 43-50.
PDB code: 1h38
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.