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PDBsum entry 1r5u
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protein metals Protein-protein interface(s) links
Transcription PDB id
1r5u

 

 

 

 

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JSmol PyMol  
Contents
Protein chains
1380 a.a. *
1097 a.a. *
266 a.a. *
214 a.a. *
84 a.a. *
133 a.a. *
118 a.a. *
65 a.a. *
114 a.a. *
46 a.a. *
86 a.a. *
Metals
_MG
_ZN ×9
* Residue conservation analysis
PDB id:
1r5u
Name: Transcription
Title: RNA polymerase ii tfiib complex
Structure: DNA-directed RNA polymerase ii largest subunit. Chain: a. Synonym: b220. DNA-directed RNA polymerase ii 140 kda polypeptide. Chain: b. Synonym: b150, RNA polymerase ii subunit 2. DNA-directed RNA polymerase ii 45 kda polypeptide. Chain: c. Synonym: b44.5.
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Strain: delta-rpb4. Gene: sua7. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Undecamer (from PQS)
Resolution:
4.50Å     R-factor:   0.345     R-free:   0.373
Authors: D.A.Bushnell,K.D.Westover,R.Davis,R.D.Kornberg
Key ref:
D.A.Bushnell et al. (2004). Structural basis of transcription: an RNA polymerase II-TFIIB cocrystal at 4.5 Angstroms. Science, 303, 983-988. PubMed id: 14963322 DOI: 10.1126/science.1090838
Date:
13-Oct-03     Release date:   17-Feb-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P04050  (RPB1_YEAST) -  DNA-directed RNA polymerase II subunit RPB1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		1733 a.a.
1380 a.a.
Protein chain
Pfam   ArchSchema ?
P08518  (RPB2_YEAST) -  DNA-directed RNA polymerase II subunit RPB2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		1224 a.a.
1097 a.a.
Protein chain
Pfam   ArchSchema ?
P16370  (RPB3_YEAST) -  DNA-directed RNA polymerase II subunit RPB3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		146 a.a.
133 a.a.
Protein chain
Pfam   ArchSchema ?
P27999  (RPB9_YEAST) -  DNA-directed RNA polymerase II subunit RPB9 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		122 a.a.
118 a.a.
Protein chain
Pfam   ArchSchema ?
P22139  (RPAB5_YEAST) -  DNA-directed RNA polymerases I, II, and III subunit RPABC5 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		70 a.a.
65 a.a.
Protein chain
Pfam   ArchSchema ?
P38902  (RPB11_YEAST) -  DNA-directed RNA polymerase II subunit RPB11 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		70 a.a.
46 a.a.
Protein chain
No UniProt id for this chain
Struc: 86 a.a.
Key:    PfamA domain  Secondary structure

 Enzyme reactions 
   Enzyme class: Chains A, B, C, E, F, H, I, J, K, L: E.C.2.7.7.6  - DNA-directed Rna polymerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate
RNA(n)
 + ribonucleoside 5'-triphosphate
 = RNA(n+1)
 + diphosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    Added reference    
 
 
DOI no: 10.1126/science.1090838 Science 303:983-988 (2004)
PubMed id: 14963322  
 
 
Structural basis of transcription: an RNA polymerase II-TFIIB cocrystal at 4.5 Angstroms.
D.A.Bushnell, K.D.Westover, R.E.Davis, R.D.Kornberg.
 
  ABSTRACT  
 
The structure of the general transcription factor IIB (TFIIB) in a complex with RNA polymerase II reveals three features crucial for transcription initiation: an N-terminal zinc ribbon domain of TFIIB that contacts the "dock" domain of the polymerase, near the path of RNA exit from a transcribing enzyme; a "finger" domain of TFIIB that is inserted into the polymerase active center; and a C-terminal domain, whose interaction with both the polymerase and with a TATA box-binding protein (TBP)-promoter DNA complex orients the DNA for unwinding and transcription. TFIIB stabilizes an early initiation complex, containing an incomplete RNA-DNA hybrid region. It may interact with the template strand, which sets the location of the transcription start site, and may interfere with RNA exit, which leads to abortive initiation or promoter escape. The trajectory of promoter DNA determined by the C-terminal domain of TFIIB traverses sites of interaction with TFIIE, TFIIF, and TFIIH, serving to define their roles in the transcription initiation process.
 
  Selected figure(s)  
 
Figure 4.
Fig. 4. Interaction of the B finger domain of TFIIB[N] with DNA template and RNA transcript. A stereo pair is shown, including the B finger domain from the pol II-TFIIB[N] structure, RNA-DNA hybrid helix from the pol II transcribing complex structure (5), and active site Mg ion. Color code is shown below. 		Figure 5.
Fig. 5. Stabilization of a transcription initiation complex, containing a short transcript, by TFIIB. (A) A single strand of DNA was bound to the surface of a Biacore Biosensor chip. Combinations of pol II, TFIIB, and a five-residue RNA complementary to the DNA were applied as indicated, and the change in refractive index near the chip surface, in resonance units (ru), was measured as a function of time. (B) Same as (A) but with nine-residue RNA.
 
  The above figures are reprinted by permission from the AAAs: Science (2004, 303, 983-988) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
20851833 S.C.Wiesler, and R.O.Weinzierl (2011).
The linker domain of basal transcription factor TFIIB controls distinct recruitment and transcription stimulation functions.
  Nucleic Acids Res, 39, 464-474.  
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.  
20369017 E.Samorodnitsky, and B.F.Pugh (2010).
Genome-wide modeling of transcription preinitiation complex disassembly mechanisms using ChIP-chip data.
  PLoS Comput Biol, 6, e1000733.  
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.  
20154708 G.Cai, T.Imasaki, K.Yamada, F.Cardelli, Y.Takagi, and F.J.Asturias (2010).
Mediator head module structure and functional interactions.
  Nat Struct Mol Biol, 17, 273-279.  
20033062 J.Eichner, H.T.Chen, L.Warfield, and S.Hahn (2010).
Position of the general transcription factor TFIIF within the RNA polymerase II transcription preinitiation complex.
  EMBO J, 29, 706-716.  
20008320 S.Paratkar, and S.S.Patel (2010).
Mitochondrial transcription factor Mtf1 traps the unwound non-template strand to facilitate open complex formation.
  J Biol Chem, 285, 3949-3956.  
20152149 W.H.Chang, M.T.Chiu, C.Y.Chen, C.F.Yen, Y.C.Lin, Y.P.Weng, J.C.Chang, Y.M.Wu, H.Cheng, J.Fu, and I.P.Tu (2010).
Zernike phase plate cryoelectron microscopy facilitates single particle analysis of unstained asymmetric protein complexes.
  Structure, 18, 17-27.  
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
20226668 Y.Wang, J.A.Fairley, and S.G.Roberts (2010).
Phosphorylation of TFIIB links transcription initiation and termination.
  Curr Biol, 20, 548-553.  
  19514890 B.J.Venters, and B.F.Pugh (2009).
How eukaryotic genes are transcribed.
  Crit Rev Biochem Mol Biol, 44, 117-141.  
19666603 B.S.Ibrahim, N.Kanneganti, G.E.Rieckhof, A.Das, D.V.Laurents, J.B.Palenchar, V.Bellofatto, and D.A.Wah (2009).
Structure of the C-terminal domain of transcription factor IIB from Trypanosoma brucei.
  Proc Natl Acad Sci U S A, 106, 13242-13247.
PDB code: 3h4c
19204718 C.Jiang, and B.F.Pugh (2009).
Nucleosome positioning and gene regulation: advances through genomics.
  Nat Rev Genet, 10, 161-172.  
19604473 C.Oubridge, D.A.Krummel, A.K.Leung, J.Li, and K.Nagai (2009).
Interpreting a low resolution map of human U1 snRNP using anomalous scatterers.
  Structure, 17, 930-938.  
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.  
19896365 D.G.Vassylyev (2009).
Elongation by RNA polymerase: a race through roadblocks.
  Curr Opin Struct Biol, 19, 691-700.  
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
19913479 H.Elmlund, V.Baraznenok, T.Linder, Z.Szilagyi, R.Rofougaran, A.Hofer, H.Hebert, M.Lindahl, and C.M.Gustafsson (2009).
Cryo-EM reveals promoter DNA binding and conformational flexibility of the general transcription factor TFIID.
  Structure, 17, 1442-1452.  
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
19933150 J.P.Lainé, B.N.Singh, S.Krishnamurthy, and M.Hampsey (2009).
A physiological role for gene loops in yeast.
  Genes Dev, 23, 2604-2609.  
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.  
  19847957 N.Kresge, R.D.Simoni, R.L.Hill, and R.Kornberg (2009).
100 years of biochemistry and molecular biology. The decade-long pursuit of a reconstituted yeast transcription system: the work of Roger D. Kornberg.
  J Biol Chem, 284, e18-e20.  
19208641 R.Brem, F.Li, and P.Karran (2009).
Reactive oxygen species generated by thiopurine/UVA cause irreparable transcription-blocking DNA lesions.
  Nucleic Acids Res, 37, 1951-1961.  
19924201 S.Hahn (2009).
Structural biology: New beginnings for transcription.
  Nature, 462, 292-293.  
19460096 S.Paytubi, and M.F.White (2009).
The crenarchaeal DNA damage-inducible transcription factor B paralogue TFB3 is a general activator of transcription.
  Mol Microbiol, 72, 1487-1499.  
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
19387772 Z.H.Yan, X.L.Gong, X.B.Guo, M.Xu, Z.R.Ren, and Y.T.Zeng (2009).
Association of differential and site-dependent CpG methylation and diverse expression of DNA methyltransferases with the tissue-specific expression of human beta-globin gene in transgenic mice.
  Int J Hematol, 89, 414-421.  
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
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.  
18468900 F.Werner (2008).
Structural evolution of multisubunit RNA polymerases.
  Trends Microbiol, 16, 247-250.  
18852287 G.S.Yochum, R.Cleland, and R.H.Goodman (2008).
A genome-wide screen for beta-catenin binding sites identifies a downstream enhancer element that controls c-Myc gene expression.
  Mol Cell Biol, 28, 7368-7379.  
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.  
18846104 J.L.Corden (2008).
Yeast Pol II start-site selection: the long and the short of it.
  EMBO Rep, 9, 1084-1086.  
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.  
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
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.  
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.  
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.  
19008886 M.Fuxreiter, P.Tompa, I.Simon, V.N.Uversky, J.C.Hansen, and F.J.Asturias (2008).
Malleable machines take shape in eukaryotic transcriptional regulation.
  Nat Chem Biol, 4, 728-737.  
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.  
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
17965161 M.Micorescu, S.Grünberg, A.Franke, P.Cramer, M.Thomm, and M.Bartlett (2008).
Archaeal transcription: function of an alternative transcription factor B from Pyrococcus furiosus.
  J Bacteriol, 190, 157-167.  
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
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.  
18218714 S.Akashi, S.Nagakura, S.Yamamoto, M.Okuda, Y.Ohkuma, and Y.Nishimura (2008).
Structural characterization of human general transcription factor TFIIF in solution.
  Protein Sci, 17, 389-400.  
18668124 S.Imamura, M.Hanaoka, and K.Tanaka (2008).
The plant-specific TFIIB-related protein, pBrp, is a general transcription factor for RNA polymerase I.
  EMBO J, 27, 2317-2327.  
19018097 S.M.Soltis, A.E.Cohen, A.Deacon, T.Eriksson, A.González, S.McPhillips, H.Chui, P.Dunten, M.Hollenbeck, I.Mathews, M.Miller, P.Moorhead, R.P.Phizackerley, C.Smith, J.Song, H.van dem Bedem, P.Ellis, P.Kuhn, T.McPhillips, N.Sauter, K.Sharp, I.Tsyba, and G.Wolf (2008).
New paradigm for macromolecular crystallography experiments at SSRL: automated crystal screening and remote data collection.
  Acta Crystallogr D Biol Crystallogr, 64, 1210-1221.  
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.  
18320553 S.Pourshahian, and P.A.Limbach (2008).
Application of fractional mass for the identification of peptide-oligonucleotide cross-links by mass spectrometry.
  J Mass Spectrom, 43, 1081-1088.  
18564169 W.Guo, Y.P.Zhao, Y.G.Jiang, R.W.Wang, L.Hong, and D.M.Fan (2008).
ZNRD1 might mediate UV irradiation related DNA damage and repair in human esophageal cancer cells by regulation of ERCC1.
  Dis Esophagus, 21, 730-736.  
18582212 Y.Han, L.Hong, J.Qiu, L.Qiao, C.Zhong, T.Xue, and M.Wang (2008).
Preparation and characterization of a novel monoclonal antibody specific to human NOB1 protein.
  Hybridoma (Larchmt), 27, 187-190.  
17709385 A.C.D'Alessio, I.C.Weaver, and M.Szyf (2007).
Acetylation-induced transcription is required for active DNA demethylation in methylation-silenced genes.
  Mol Cell Biol, 27, 7462-7474.  
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.  
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.  
17697097 F.Werner (2007).
Structure and function of archaeal RNA polymerases.
  Mol Microbiol, 65, 1395-1404.  
17997859 G.S.Yochum, V.Rajaraman, R.Cleland, and S.McWeeney (2007).
Localization of TFIIB binding regions using serial analysis of chromatin occupancy.
  BMC Mol Biol, 8, 102.  
17632521 H.T.Chen, L.Warfield, and S.Hahn (2007).
The positions of TFIIF and TFIIE in the RNA polymerase II transcription preinitiation complex.
  Nat Struct Mol Biol, 14, 696-703.  
17676030 P.Cramer (2007).
Finding the right spot to start transcription.
  Nat Struct Mol Biol, 14, 686-687.  
17670940 R.D.Kornberg (2007).
The molecular basis of eukaryotic transcription.
  Proc Natl Acad Sci U S A, 104, 12955-12961.  
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.  
17593382 W.Deng, and S.G.Roberts (2007).
TFIIB and the regulation of transcription by RNA polymerase II.
  Chromosoma, 116, 417-429.  
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
16778763 A.R.Hieb, S.Baran, J.A.Goodrich, and J.F.Kugel (2006).
An 8 nt RNA triggers a rate-limiting shift of RNA polymerase II complexes into elongation.
  EMBO J, 25, 3100-3109.  
16936696 A.Saunders, L.J.Core, and J.T.Lis (2006).
Breaking barriers to transcription elongation.
  Nat Rev Mol Cell Biol, 7, 557-567.  
16554554 B.Schimanski, J.Brandenburg, T.N.Nguyen, M.J.Caimano, and A.Günzl (2006).
A TFIIB-like protein is indispensable for spliced leader RNA gene transcription in Trypanosoma brucei.
  Nucleic Acids Res, 34, 1676-1684.  
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
16916456 J.Ponjavic, B.Lenhard, C.Kai, J.Kawai, P.Carninci, Y.Hayashizaki, and A.Sandelin (2006).
Transcriptional and structural impact of TATA-initiation site spacing in mammalian core promoters.
  Genome Biol, 7, R78.  
17036198 J.Wang, X.Lv, J.Shi, and X.Hu (2006).
Ceramide induces apoptosis via a peroxisome proliferator-activated receptor gamma-dependent pathway.
  Apoptosis, 11, 2043-2052.  
16878124 L.M.Elsby, A.J.O'Donnell, L.M.Green, A.D.Sharrocks, and S.G.Roberts (2006).
Assembly of transcription factor IIB at a promoter in vivo requires contact with RNA polymerase II.
  EMBO Rep, 7, 898-903.  
16826228 M.Hampsey (2006).
The Pol II initiation complex: finding a place to start.
  Nat Struct Mol Biol, 13, 564-566.  
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
17146456 P.Cramer (2006).
Deciphering the RNA polymerase II structure: a personal perspective.
  Nat Struct Mol Biol, 13, 1042-1044.  
17174884 R.Landick, and R.Kornberg (2006).
A long time in the making--the Nobel Prize for RNA polymerase.
  Cell, 127, 1087-1090.  
17098194 S.A.Kostek, P.Grob, S.De Carlo, J.S.Lipscomb, F.Garczarek, and E.Nogales (2006).
Molecular architecture and conformational flexibility of human RNA polymerase II.
  Structure, 14, 1691-1700.  
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.  
16880507 Y.Liao, R.D.Moir, and I.M.Willis (2006).
Interactions of Brf1 peptides with the tetratricopeptide repeat-containing subunit of TFIIIC inhibit and promote preinitiation complex assembly.
  Mol Cell Biol, 26, 5946-5956.  
16245355 Y.Yamazaki, T.C.Fujita, E.W.Low, V.B.Alarcón, R.Yanagimachi, and Y.Marikawa (2006).
Gradual DNA demethylation of the Oct4 promoter in cloned mouse embryos.
  Mol Reprod Dev, 73, 180-188.  
16227591 A.Saxena, B.Ma, L.Schramm, and N.Hernandez (2005).
Structure-function analysis of the human TFIIB-related factor II protein reveals an essential role for the C-terminal domain in RNA polymerase III transcription.
  Mol Cell Biol, 25, 9406-9418.  
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.  
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.  
15612920 C.Zaros, and P.Thuriaux (2005).
Rpc25, a conserved RNA polymerase III subunit, is critical for transcription initiation.
  Mol Microbiol, 55, 104-114.  
15916593 E.P.Geiduschek, and M.Ouhammouch (2005).
Archaeal transcription and its regulators.
  Mol Microbiol, 56, 1397-1407.  
16135821 F.Werner, and R.O.Weinzierl (2005).
Direct modulation of RNA polymerase core functions by basal transcription factors.
  Mol Cell Biol, 25, 8344-8355.  
15971229 G.Cavelier, and D.Anastassiou (2005).
Phenotype analysis using network motifs derived from changes in regulatory network dynamics.
  Proteins, 60, 525-546.  
15888545 J.L.Hodges, J.H.Leslie, N.Mosammaparast, Y.Guo, J.Shabanowitz, D.F.Hunt, and L.F.Pemberton (2005).
Nuclear import of TFIIB is mediated by Kap114p, a karyopherin with multiple cargo-binding domains.
  Mol Biol Cell, 16, 3200-3210.  
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.  
15743411 K.Hayashi, T.Watanabe, A.Tanaka, T.Furumoto, C.Sato-Tsuchiya, M.Kimura, M.Yokoi, A.Ishihama, F.Hanaoka, and Y.Ohkuma (2005).
Studies of Schizosaccharomyces pombe TFIIE indicate conformational and functional changes in RNA polymerase II at transcription initiation.
  Genes Cells, 10, 207-224.  
15652480 L.Chen, and J.Widom (2005).
Mechanism of transcriptional silencing in yeast.
  Cell, 120, 37-48.  
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.  
16249119 M.S.Bartlett (2005).
Determinants of transcription initiation by archaeal RNA polymerase.
  Curr Opin Microbiol, 8, 677-684.  
16252250 R.L.Rich, and D.G.Myszka (2005).
Survey of the year 2004 commercial optical biosensor literature.
  J Mol Recognit, 18, 431-478.  
15574517 S.O.Gudima, J.Chang, and J.M.Taylor (2005).
Reconstitution in cultured cells of replicating HDV RNA from pairs of less than full-length RNAs.
  RNA, 11, 90-98.  
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
15937491 Y.C.Lin, W.S.Choi, and J.D.Gralla (2005).
TFIIH XPB mutants suggest a unified bacterial-like mechanism for promoter opening but not escape.
  Nat Struct Mol Biol, 12, 603-607.  
16184598 Y.Itoh, S.Unzai, M.Sato, A.Nagadoi, M.Okuda, Y.Nishimura, and S.Akashi (2005).
Investigation of molecular size of transcription factor TFIIE in solution.
  Proteins, 61, 633-641.  
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.  
15523475 F.J.Asturias (2004).
Another piece in the transcription initiation puzzle.
  Nat Struct Mol Biol, 11, 1031-1033.  
15093825 F.J.Asturias (2004).
RNA polymerase II structure, and organization of the preinitiation complex.
  Curr Opin Struct Biol, 14, 121-129.  
15610738 H.Kettenberger, K.J.Armache, and P.Cramer (2004).
Complete RNA polymerase II elongation complex structure and its interactions with NTP and TFIIS.
  Mol Cell, 16, 955-965.
PDB codes: 1y1v 1y1w 1y1y 1y77
15479635 H.T.Chen, and S.Hahn (2004).
Mapping the location of TFIIB within the RNA polymerase II transcription preinitiation complex: a model for the structure of the PIC.
  Cell, 119, 169-180.  
15574497 N.N.Batada, K.D.Westover, D.A.Bushnell, M.Levitt, and R.D.Kornberg (2004).
Diffusion of nucleoside triphosphates and role of the entry site to the RNA polymerase II active center.
  Proc Natl Acad Sci U S A, 101, 17361-17364.  
15470504 P.C.Burrows, K.Severinov, M.Buck, and S.R.Wigneshweraraj (2004).
Reorganisation of an RNA polymerase-promoter DNA complex for DNA melting.
  EMBO J, 23, 4253-4263.  
15114340 S.Hahn (2004).
Structure and mechanism of the RNA polymerase II transcription machinery.
  Nat Struct Mol Biol, 11, 394-403.  
15470503 S.R.Wigneshweraraj, P.C.Burrows, S.Nechaev, N.Zenkin, K.Severinov, and M.Buck (2004).
Regulated communication between the upstream face of RNA polymerase and the beta' subunit jaw domain.
  EMBO J, 23, 4264-4274.  
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 code is shown on the right.

 

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