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PDBsum entry 1y1w

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protein dna_rna metals Protein-protein interface(s) links
Transcription,transferase/DNA-RNA hybrid PDB id
1y1w
Jmol PyMol
Contents
Protein chains
1416 a.a. *
1112 a.a. *
266 a.a. *
177 a.a. *
214 a.a. *
84 a.a. *
171 a.a. *
133 a.a. *
119 a.a. *
65 a.a. *
114 a.a. *
46 a.a. *
DNA/RNA
Metals
_ZN ×8
_MG
* Residue conservation analysis
PDB id:
1y1w
Name: Transcription,transferase/DNA-RNA hybrid
Title: Complete RNA polymerase ii elongation complex
Structure: 5'- d(p Ap Gp Tp Ap Cp Tp Tp Ap Cp Gp Cp Cp Tp Gp Gp Tp Cp Ap T )-3'. Chain: t. Engineered: yes. 5'-d( Ap Ap Gp Tp Ap Cp T)-3'. Chain: n. Engineered: yes. 5'-r( Ap Ap Gp Ap Cp Cp Ap Gp Gp C)-3'.
Source: Synthetic: yes. Other_details: synthetic oligonucleotide. Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Organism_taxid: 4932
Biol. unit: 15mer (from PQS)
Resolution:
4.00Å     R-factor:   0.253     R-free:   0.276
Authors: P.Cramer,H.Kettenberger,K.-J.Armache
Key ref:
H.Kettenberger et al. (2004). Complete RNA polymerase II elongation complex structure and its interactions with NTP and TFIIS. Mol Cell, 16, 955-965. PubMed id: 15610738 DOI: 10.1016/j.molcel.2004.11.040
Date:
19-Nov-04     Release date:   04-Jan-05    
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.
1416 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.
1112 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 ?
P20433  (RPB4_YEAST) -  DNA-directed RNA polymerase II subunit RPB4
Seq:
Struc:
221 a.a.
177 a.a.
Protein chain
Pfam   ArchSchema ?
P20434  (RPAB1_YEAST) -  DNA-directed RNA polymerases I, II, and III subunit RPABC1
Seq:
Struc:
215 a.a.
214 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 ?
P34087  (RPB7_YEAST) -  DNA-directed RNA polymerase II subunit RPB7
Seq:
Struc:
171 a.a.
171 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.
119 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

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   12 terms 
  Biological process     transcription, RNA-dependent   25 terms 
  Biochemical function     RNA polymerase II activity     19 terms  

 

 
DOI no: 10.1016/j.molcel.2004.11.040 Mol Cell 16:955-965 (2004)
PubMed id: 15610738  
 
 
Complete RNA polymerase II elongation complex structure and its interactions with NTP and TFIIS.
H.Kettenberger, K.J.Armache, P.Cramer.
 
  ABSTRACT  
 
The crystal structure of the complete 12 subunit RNA polymerase (pol) II bound to a transcription bubble and product RNA reveals incoming template and nontemplate DNA, a seven base pair DNA/RNA hybrid, and three nucleotides each of separating DNA and RNA. The complex adopts the posttranslocation state and accommodates a cocrystallized nucleoside triphosphate (NTP) substrate. The NTP binds in the active site pore at a position to interact with a DNA template base. Residues surrounding the NTP are conserved in all cellular RNA polymerases, suggesting a universal mechanism of NTP selection and incorporation. DNA-DNA and DNA-RNA strand separation may be explained by pol II-induced duplex distortions. Four protein loops partition the active center cleft, contribute to embedding the hybrid, prevent strand reassociation, and create an RNA exit tunnel. Binding of the elongation factor TFIIS realigns RNA in the active center, possibly converting the elongation complex to an alternative state less prone to stalling.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. Conservation and Compartmentalization of the Polymerase Cleft(A) Overall structure of the pol II-bubble-RNA complex. The complete pol II is shown as a molecular surface, and nucleic acid backbones are drawn as ribbons. The view corresponds to the front view (Cramer et al. 2000 and Cramer et al. 2001). A dashed line indicates the slice plane used to create the views in (C).(B) Top view of the model in (A). Pol II loops are outlined that partition the enzyme cleft. During transcription elongation, DNA enters from the right. Previously proposed RNA exit grooves are labeled 1 and 2.(C) Conservation of nucleic-acid interaction surfaces. The model in (A) was intersected along the plane indicated in (A), and the resulting halves were rotated by 90° around a vertical axis in opposite directions. The molecular surface of residues within 8 Å distance from nucleic acids is colored in beige. Residues that are invariant and conserved between pol I, II, and III are highlighted in dark and light green, respectively. Pol II elements that contact nucleic acids and partition the enzyme cleft are outlined.
Figure 6.
Figure 6. TFIIS-Induced RNA RealignmentSelected elements in the pol II active center that move upon TFIIS binding are shown. The bridge helix, DNA, and RNA in the pol II-bubble-RNA-TFIIS complex are in green, blue, and red, respectively. The TFIIS hairpin is in orange with the two acidic functionally essential and invariant residues in green. Nucleic acids in the pol II-bubble-RNA complex structure after superposition of residues in the active site aspartate loop or in switch 2 are shown in beige and gray, respectively. Switch 2 moves slightly upon TFIIS binding (Kettenberger et al., 2003), explaining the difference in the two superpositions.
 
  The above figures are reprinted by permission from Cell Press: Mol Cell (2004, 16, 955-965) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22751016 S.Grünberg, L.Warfield, and S.Hahn (2012).
Architecture of the RNA polymerase II preinitiation complex and mechanism of ATP-dependent promoter opening.
  Nat Struct Mol Biol, 19, 788-796.  
21346759 A.C.Cheung, and P.Cramer (2011).
Structural basis of RNA polymerase II backtracking, arrest and reactivation.
  Nature, 471, 249-253.
PDB codes: 3po2 3po3
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.  
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.  
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.  
21463690 R.J.Hall, E.Nogales, and R.M.Glaeser (2011).
Accurate modeling of single-particle cryo-EM images quantitates the benefits expected from using Zernike phase contrast.
  J Struct Biol, 174, 468-475.  
21447716 S.R.Kennedy, and D.A.Erie (2011).
Templated nucleoside triphosphate binding to a noncatalytic site on RNA polymerase regulates transcription.
  Proc Natl Acad Sci U S A, 108, 6079-6084.  
19906731 A.Hirtreiter, D.Grohmann, and F.Werner (2010).
Molecular mechanisms of RNA polymerase--the F/E (RPB4/7) complex is required for high processivity in vitro.
  Nucleic Acids Res, 38, 585-596.  
19567268 C.Domecq, M.Kireeva, J.Archambault, M.Kashlev, B.Coulombe, and Z.F.Burton (2010).
Site-directed mutagenesis, purification and assay of Saccharomyces cerevisiae RNA polymerase II.
  Protein Expr Purif, 69, 83-90.  
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.  
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.  
  20473037 D.Grohmann, and F.Werner (2010).
Hold on!: RNA polymerase interactions with the nascent RNA modulate transcription elongation and termination.
  RNA Biol, 7, 310-315.  
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.  
20132437 G.A.Belogurov, A.Sevostyanova, V.Svetlov, and I.Artsimovitch (2010).
Functional regions of the N-terminal domain of the antiterminator RfaH.
  Mol Microbiol, 76, 286-301.  
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.  
  20509894 J.Farlow, M.A.Ichou, J.Huggins, and S.Ibrahim (2010).
Comparative whole genome sequence analysis of wild-type and cidofovir-resistant monkeypoxvirus.
  Virol J, 7, 110.  
19966797 J.Zhang, M.Palangat, and R.Landick (2010).
Role of the RNA polymerase trigger loop in catalysis and pausing.
  Nat Struct Mol Biol, 17, 99.  
20453859 K.D.Meyer, S.C.Lin, C.Bernecky, Y.Gao, and D.J.Taatjes (2010).
p53 activates transcription by directing structural shifts in Mediator.
  Nat Struct Mol Biol, 17, 753-760.  
20482321 P.Cramer (2010).
Towards molecular systems biology of gene transcription and regulation.
  Biol Chem, 391, 731-735.  
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
20075920 V.Epshtein, D.Dutta, J.Wade, and E.Nudler (2010).
An allosteric mechanism of Rho-dependent transcription termination.
  Nature, 463, 245-249.  
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.  
20459653 Y.Yuzenkova, A.Bochkareva, V.R.Tadigotla, M.Roghanian, S.Zorov, K.Severinov, and N.Zenkin (2010).
Stepwise mechanism for transcription fidelity.
  BMC Biol, 8, 54.  
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.  
19605532 A.C.Rhee, B.H.Somerlot, N.Parimi, and J.M.Gott (2009).
Distinct roles for sequences upstream of and downstream from Physarum editing sites.
  RNA, 15, 1753-1765.  
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
19478184 D.Wang, D.A.Bushnell, X.Huang, K.D.Westover, M.Levitt, and R.D.Kornberg (2009).
Structural basis of transcription: backtracked RNA polymerase II at 3.4 angstrom resolution.
  Science, 324, 1203-1206.
PDB codes: 3gtg 3gtj 3gtk 3gtl 3gtm 3gto 3gtp 3gtq
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
19758983 G.E.Damsma, and P.Cramer (2009).
Molecular basis of transcriptional mutagenesis at 8-oxoguanine.
  J Biol Chem, 284, 31658-31663.
PDB codes: 3i4m 3i4n
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.  
19560423 J.F.Sydow, F.Brueckner, A.C.Cheung, G.E.Damsma, S.Dengl, E.Lehmann, D.Vassylyev, and P.Cramer (2009).
Structural basis of transcription: mismatch-specific fidelity mechanisms and paused RNA polymerase II with frayed RNA.
  Mol Cell, 34, 710-721.
PDB codes: 3hou 3hov 3how 3hox 3hoy 3hoz
19416863 M.L.Kireeva, and M.Kashlev (2009).
Mechanism of sequence-specific pausing of bacterial RNA polymerase.
  Proc Natl Acad Sci U S A, 106, 8900-8905.  
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.  
19935686 O.I.Kulaeva, D.A.Gaykalova, N.A.Pestov, V.V.Golovastov, D.G.Vassylyev, I.Artsimovitch, and V.M.Studitsky (2009).
Mechanism of chromatin remodeling and recovery during passage of RNA polymerase II.
  Nat Struct Mol Biol, 16, 1272-1278.  
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
19535338 S.Dengl, and P.Cramer (2009).
Torpedo Nuclease Rat1 Is Insufficient to Terminate RNA Polymerase II in Vitro.
  J Biol Chem, 284, 21270-21279.
PDB code: 3h3v
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
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.  
18815126 A.Ujvári, F.K.Hsieh, S.W.Luse, V.M.Studitsky, and D.S.Luse (2008).
Histone N-terminal Tails Interfere with Nucleosome Traversal by RNA Polymerase II.
  J Biol Chem, 283, 32236-32243.  
19090964 C.D.Kaplan, and R.D.Kornberg (2008).
A bridge to transcription by RNA polymerase.
  J Biol, 7, 39.  
18514566 C.S.Pikaard, J.R.Haag, T.Ream, and A.T.Wierzbicki (2008).
Roles of RNA polymerase IV in gene silencing.
  Trends Plant Sci, 13, 390-397.  
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
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.  
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.  
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.  
17991737 J.R.Haanstra, M.Stewart, V.D.Luu, A.van Tuijl, H.V.Westerhoff, C.Clayton, and B.M.Bakker (2008).
Control and Regulation of Gene Expression: QUANTITATIVE ANALYSIS OF THE EXPRESSION OF PHOSPHOGLYCERATE KINASE IN BLOODSTREAM FORM TRYPANOSOMA BRUCEI.
  J Biol Chem, 283, 2495-2507.  
18086892 L.Zhang, A.G.Fletcher, V.Cheung, F.Winston, and L.A.Stargell (2008).
Spn1 regulates the recruitment of Spt6 and the Swi/Snf complex during transcriptional activation by RNA polymerase II.
  Mol Cell Biol, 28, 1393-1403.  
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.  
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.  
18627464 P.Uzureau, J.P.Daniels, D.Walgraffe, B.Wickstead, E.Pays, K.Gull, and L.Vanhamme (2008).
Identification and characterization of two trypanosome TFIIS proteins exhibiting particular domain architectures and differential nuclear localizations.
  Mol Microbiol, 69, 1121-1136.  
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.  
17580305 A.McAlinden, L.Liang, Y.Mukudai, T.Imamura, and L.J.Sandell (2007).
Nuclear protein TIA-1 regulates COL2A1 alternative splicing and interacts with precursor mRNA and genomic DNA.
  J Biol Chem, 282, 24444-24454.  
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.  
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
17581591 D.G.Vassylyev, M.N.Vassylyeva, J.Zhang, M.Palangat, I.Artsimovitch, and R.Landick (2007).
Structural basis for substrate loading in bacterial RNA polymerase.
  Nature, 448, 163-168.
PDB codes: 2o5j 2ppb
18064834 E.A.Kashkina, M.V.Anikin, W.T.McAllister, N.Kochetkov, and D.E.Temyakov (2007).
Determination of the melting site of the DNA duplex in the active center of bacterial RNA-polymerase by fluorescence quenching technique.
  Dokl Biochem Biophys, 416, 285-289.  
17526498 E.Kashkina, M.Anikin, F.Brueckner, E.Lehmann, S.N.Kochetkov, W.T.McAllister, P.Cramer, and D.Temiakov (2007).
Multisubunit RNA polymerases melt only a single DNA base pair downstream of the active site.
  J Biol Chem, 282, 21578-21582.  
18004386 E.Lehmann, F.Brueckner, and P.Cramer (2007).
Molecular basis of RNA-dependent RNA polymerase II activity.
  Nature, 450, 445-449.
PDB codes: 2r92 2r93
17290000 F.Brueckner, U.Hennecke, T.Carell, and P.Cramer (2007).
CPD damage recognition by transcribing RNA polymerase II.
  Science, 315, 859-862.
PDB codes: 2ja5 2ja6 2ja7 2ja8
17434131 G.A.Belogurov, M.N.Vassylyeva, V.Svetlov, S.Klyuyev, N.V.Grishin, D.G.Vassylyev, and I.Artsimovitch (2007).
Structural basis for converting a general transcription factor into an operon-specific virulence regulator.
  Mol Cell, 26, 117-129.
PDB code: 2oug
17994106 G.E.Damsma, A.Alt, F.Brueckner, T.Carell, and P.Cramer (2007).
Mechanism of transcriptional stalling at cisplatin-damaged DNA.
  Nat Struct Mol Biol, 14, 1127-1133.
PDB code: 2r7z
17537816 H.Gaillard, R.E.Wellinger, and A.Aguilera (2007).
A new connection of mRNP biogenesis and export with transcription-coupled repair.
  Nucleic Acids Res, 35, 3893-3906.  
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.  
17625551 P.Cramer (2007).
Gene transcription: extending the message.
  Nature, 448, 142-143.  
17267688 S.Devaux, S.Kelly, L.Lecordier, B.Wickstead, D.Perez-Morga, E.Pays, L.Vanhamme, and K.Gull (2007).
Diversification of function by different isoforms of conventionally shared RNA polymerase subunits.
  Mol Biol Cell, 18, 1293-1301.  
18158897 V.Epshtein, C.J.Cardinale, A.E.Ruckenstein, S.Borukhov, and E.Nudler (2007).
An allosteric path to transcription termination.
  Mol Cell, 28, 991.  
17875640 Y.Xiong, and Z.F.Burton (2007).
A tunable ratchet driving human RNA polymerase II translocation adjusted by accurately templated nucleoside triphosphates loaded at downstream sites and by elongation factors.
  J Biol Chem, 282, 36582-36592.  
17584298 Y.Yamaguchi, T.Mura, S.Chanarat, S.Okamoto, and H.Handa (2007).
Hepatitis delta antigen binds to the clamp of RNA polymerase II and affects transcriptional fidelity.
  Genes Cells, 12, 863-875.  
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
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
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.  
16317791 D.W.Heinz, M.S.Weiss, and K.U.Wendt (2006).
Biomacromolecular interactions, assemblies and machines: a structural view.
  Chembiochem, 7, 203-208.  
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 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.  
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.  
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.  
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.  
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.  
16873663 N.Zenkin, Y.Yuzenkova, and K.Severinov (2006).
Transcript-assisted transcriptional proofreading.
  Science, 313, 518-520.  
16628221 O.Laptenko, S.S.Kim, J.Lee, M.Starodubtseva, F.Cava, J.Berenguer, X.P.Kong, and S.Borukhov (2006).
pH-dependent conformational switch activates the inhibitor of transcription elongation.
  EMBO J, 25, 2131-2141.
PDB code: 2f23
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
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.  
16621791 S.F.Holmes, T.J.Santangelo, C.K.Cunningham, J.W.Roberts, and D.A.Erie (2006).
Kinetic investigation of Escherichia coli RNA polymerase mutants that influence nucleotide discrimination and transcription fidelity.
  J Biol Chem, 281, 18677-18683.  
16511564 S.Kamtekar, A.J.Berman, J.Wang, J.M.Lázaro, M.de Vega, L.Blanco, M.Salas, and T.A.Steitz (2006).
The phi29 DNA polymerase:protein-primer structure suggests a model for the initiation to elongation transition.
  EMBO J, 25, 1335-1343.
PDB code: 2ex3
16900098 T.A.Steitz (2006).
Visualizing polynucleotide polymerase machines at work.
  EMBO J, 25, 3458-3468.  
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.  
16648364 Y.Ling, A.J.Smith, and G.T.Morgan (2006).
A sequence motif conserved in diverse nuclear proteins identifies a protein interaction domain utilised for nuclear targeting by human TFIIS.
  Nucleic Acids Res, 34, 2219-2229.  
16033533 A.Franklin, and R.V.Blanden (2005).
Hypothesis: biological role for J-C intronic matrix attachment regions in the molecular mechanism of antigen-driven somatic hypermutation.
  Immunol Cell Biol, 83, 383-391.  
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.  
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.  
16360025 D.G.Vassylyev, and I.Artsimovitch (2005).
Tracking RNA polymerase, one step at a time.
  Cell, 123, 977-979.  
16273103 D.G.Vassylyev, V.Svetlov, M.N.Vassylyeva, A.Perederina, N.Igarashi, N.Matsugaki, S.Wakatsuki, and I.Artsimovitch (2005).
Structural basis for transcription inhibition by tagetitoxin.
  Nat Struct Mol Biol, 12, 1086-1093.
PDB code: 2be5
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
15916593 E.P.Geiduschek, and M.Ouhammouch (2005).
Archaeal transcription and its regulators.
  Mol Microbiol, 56, 1397-1407.  
15591044 K.J.Armache, S.Mitterweger, A.Meinhart, and P.Cramer (2005).
Structures of complete RNA polymerase II and its subcomplex, Rpb4/7.
  J Biol Chem, 280, 7131-7134.
PDB codes: 1wcm 1y14
16147988 M.A.Freire-Picos, S.Krishnamurthy, Z.W.Sun, and M.Hampsey (2005).
Evidence that the Tfg1/Tfg2 dimer interface of TFIIF lies near the active center of the RNA polymerase II initiation complex.
  Nucleic Acids Res, 33, 5045-5052.  
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.  
16081422 R.C.Majovski, D.A.Khaperskyy, M.A.Ghazy, and A.S.Ponticelli (2005).
A functional role for the switch 2 region of yeast RNA polymerase II in transcription start site utilization and abortive initiation.
  J Biol Chem, 280, 34917-34923.  
16122417 S.Kyzer, J.Zhang, and R.Landick (2005).
Inhibition of RNA polymerase by streptolydigin: no cycling allowed.
  Cell, 122, 494-496.  
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
16049026 V.Sosunov, S.Zorov, E.Sosunova, A.Nikolaev, I.Zakeyeva, I.Bass, A.Goldfarb, V.Nikiforov, K.Severinov, and A.Mustaev (2005).
The involvement of the aspartate triad of the active center in all catalytic activities of multisubunit RNA polymerase.
  Nucleic Acids Res, 33, 4202-4211.  
16094452 Z.F.Burton, M.Feig, X.Q.Gong, C.Zhang, Y.A.Nedialkov, and Y.Xiong (2005).
NTP-driven translocation and regulation of downstream template opening by multi-subunit RNA polymerases.
  Biochem Cell Biol, 83, 486-496.  
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.

 

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