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PDBsum entry 1nt9
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protein links
Transcription, transferase PDB id
1nt9
Contents
Protein chains
1383 a.a.* *
1089 a.a.* *
266 a.a.* *
97 a.a.* *
214 a.a.* *
84 a.a.* *
169 a.a.* *
133 a.a.* *
119 a.a.* *
65 a.a.* *
114 a.a.* *
46 a.a.* *
* Residue conservation analysis
* C-alpha coords only
PDB id:
1nt9
Name: Transcription, transferase
Title: Complete 12-subunit RNA polymerase ii
Structure: DNA-directed RNA polymerase ii largest subunit. Chain: a. Synonym: rpb1. B220. DNA-directed polymerase ii second largest subunit. Chain: b. Synonym: rpb2. B150. DNA-directed RNA polymerase ii 140 kda polypeptide. DNA-directed RNA polymerase ii 45 kda polypeptide. Chain: c.
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Strain: delta-rpb4. Expressed in: escherichia coli. Expression_system_taxid: 562. Strain: delta-rpb4
Biol. unit: Dodecamer (from PQS)
Resolution:
4.20Å     R-factor:   not given    
Authors: K.-J.Armache,H.Kettenberger,P.Cramer
Key ref:
K.J.Armache et al. (2003). Architecture of initiation-competent 12-subunit RNA polymerase II. Proc Natl Acad Sci U S A, 100, 6964-6968. PubMed id: 12746495 DOI: 10.1073/pnas.1030608100
Date:
29-Jan-03     Release date:   22-Apr-03    
 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.
1383 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.
1089 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 ?
P20433  (RPB4_YEAST) -  DNA-directed RNA polymerase II subunit RPB4 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		221 a.a.
97 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 ?
P34087  (RPB7_YEAST) -  DNA-directed RNA polymerase II subunit RPB7 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		171 a.a.
169 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.
119 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.
Key:    PfamA domain  Secondary structure
* PDB and UniProt seqs differ at 13 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains A, B, C, D, E, F, G, 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: 10.1073/pnas.1030608100 Proc Natl Acad Sci U S A 100:6964-6968 (2003)
PubMed id: 12746495  
 
 
Architecture of initiation-competent 12-subunit RNA polymerase II.
K.J.Armache, H.Kettenberger, P.Cramer.
 
  ABSTRACT  
 
RNA polymerase (Pol) II consists of a 10-polypeptide catalytic core and the two-subunit Rpb4/7 complex that is required for transcription initiation. Previous structures of the Pol II core revealed a "clamp," which binds the DNA template strand via three "switch regions," and a flexible "linker" to the C-terminal repeat domain (CTD). Here we derived a model of the complete Pol II by fitting structures of the core and Rpb4/7 to a 4.2-A crystallographic electron density map. Rpb4/7 protrudes from the polymerase "upstream face," on which initiation factors assemble for promoter DNA loading. Rpb7 forms a wedge between the clamp and the linker, restricting the clamp to a closed position. The wedge allosterically prevents entry of the promoter DNA duplex into the active center cleft and induces in two switch regions a conformation poised for template-strand binding. Interaction of Rpb4/7 with the linker explains Rpb4-mediated recruitment of the CTD phosphatase to the CTD during Pol II recycling. The core-Rpb7 interaction and some functions of Rpb4/7 are apparently conserved in all eukaryotic and archaeal RNA polymerases but not in the bacterial enzyme.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. Architecture of the 12-subunit Pol II, coupling of Rpb4/7 binding and clamp closure, and upstream interaction face. (A) Ribbon model of Pol II. The view is as described for Fig. 1. Cyan spheres and a pink sphere depict eight zinc ions and an active-site magnesium ion, respectively. A black line circles the clamp. The linker to the CTD is indicated as a dashed line. In the lower-right corner, a schematic cut-away view is shown. A dashed line indicates the open clamp position observed in form 2 of the Pol II core structure (7). (B) Pol II upstream interaction face. Shown in a view of the model from the "top" (6). The circle segment is centered at the active site and has a radius that corresponds to the minimal distance between the TATA box and the transcription start site (85 Å, 25 bp). The saddle between the wall and the clamp and the assumed direction of RNA exit are indicated. A blue asterisk indicates a potential RNA-binding face of Rpb7 (15, 22). A key to subunit color is shown in the upper right corner. The figure was prepared with RIBBONS (54). 		Figure 3.
Fig. 3. Pocket-tip interaction. (A) Ribbon model of the Rpb7 tip binding with its two outermost loops (15) to the five protein regions (7) that line the pocket. The view is from the "back," roughly the reverse of that shown in Figs. 1 and 2A. Colors are as described for Fig. 2 except that switch region 5 is green. (B) Sequence alignments of protein regions are as described for A. Hs, Homo sapiens; Dm, Drosophila melanogaster; Sp, Schizosaccharomyces pombe; Sc, S. cerevisiae; Mj, Methanococcus jannaschii; Ss, Sulfolobus solfataricus. Conserved residues are highlighted. The stars below the alignments indicate invariant residues. The figure was prepared with RIBBONS (54).
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  21417597 A.Y.Park, and C.V.Robinson (2011).
Protein-nucleic acid complexes and the role of mass spectrometry in their structure determination.
  Crit Rev Biochem Mol Biol, 46, 152-164.  
21415355 J.Soutourina, S.Wydau, Y.Ambroise, C.Boschiero, and M.Werner (2011).
Direct interaction of RNA polymerase II and mediator required for transcription in vivo.
  Science, 331, 1451-1454.  
20637414 D.Elmlund, R.Davis, and H.Elmlund (2010).
Ab initio structure determination from electron microscopic images of single molecules coexisting in different functional states.
  Structure, 18, 777-786.  
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.  
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.  
  21326901 S.De Carlo, S.C.Lin, D.J.Taatjes, and A.Hoenger (2010).
Molecular basis of transcription initiation in Archaea.
  Transcr, 1, 103-111.  
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.  
19148648 A.Gentile, R.F.Ditt, F.O.Dias, M.J.Da Silva, M.C.Dornelas, and M.Menossi (2009).
Characterization of ScMat1, a putative TFIIH subunit from sugarcane.
  Plant Cell Rep, 28, 663-672.  
19880312 A.Hirata, and K.S.Murakami (2009).
Archaeal RNA polymerase.
  Curr Opin Struct Biol, 19, 724-731.  
19280431 A.Z.Ansari (2009).
Riboactivators: transcription activation by noncoding RNA.
  Crit Rev Biochem Mol Biol, 44, 50-61.  
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
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.  
19368889 G.Cai, T.Imasaki, Y.Takagi, and F.J.Asturias (2009).
Mediator structural conservation and implications for the regulation mechanism.
  Structure, 17, 559-567.  
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.  
  19478915 J.Wang, I.Dasgupta, and G.E.Fox (2009).
Many nonuniversal archaeal ribosomal proteins are found in conserved gene clusters.
  Archaea, 2, 241-251.  
19079263 L.Huang, A.M.Jones, I.Searle, K.Patel, H.Vogler, N.C.Hubner, and D.C.Baulcombe (2009).
An atypical RNA polymerase involved in RNA silencing shares small subunits with RNA polymerase II.
  Nat Struct Mol Biol, 16, 91-93.  
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
19165144 X.Peñate, D.López-Farfán, D.Landeira, A.Wentland, I.Vidal, and M.Navarro (2009).
RNA pol II subunit RPB7 is required for RNA pol I-mediated transcription in Trypanosoma brucei.
  EMBO Rep, 10, 252-257.  
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
18786148 A.Hirata, T.Kanai, T.J.Santangelo, M.Tajiri, K.Manabe, J.N.Reeve, T.Imanaka, and K.S.Murakami (2008).
Archaeal RNA polymerase subunits E and F are not required for transcription in vitro, but a Thermococcus kodakarensis mutant lacking subunit F is temperature-sensitive.
  Mol Microbiol, 70, 623-633.  
18264749 B.A.Knutson, and S.S.Broyles (2008).
Expansion of poxvirus RNA polymerase subunits sharing homology with corresponding subunits of RNA polymerase II.
  Virus Genes, 36, 307-311.  
18086878 F.Beckouet, S.Labarre-Mariotte, B.Albert, Y.Imazawa, M.Werner, O.Gadal, Y.Nogi, and P.Thuriaux (2008).
Two RNA polymerase I subunits control the binding and release of Rrn3 during transcription.
  Mol Cell Biol, 28, 1596-1605.  
18552824 F.Brueckner, and P.Cramer (2008).
Structural basis of transcription inhibition by alpha-amanitin and implications for RNA polymerase II translocation.
  Nat Struct Mol Biol, 15, 811-818.
PDB code: 2vum
18441121 J.Verma-Gaur, S.N.Rao, T.Taya, and P.Sadhale (2008).
Genomewide recruitment analysis of Rpb4, a subunit of polymerase II in Saccharomyces cerevisiae, reveals its involvement in transcription elongation.
  Eukaryot Cell, 7, 1009-1018.  
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.  
18676807 V.Goler-Baron, M.Selitrennik, O.Barkai, G.Haimovich, R.Lotan, and M.Choder (2008).
Transcription in the nucleus and mRNA decay in the cytoplasm are coupled processes.
  Genes Dev, 22, 2022-2027.  
18195044 V.M.Runner, V.Podolny, and S.Buratowski (2008).
The Rpb4 subunit of RNA polymerase II contributes to cotranscriptional recruitment of 3' processing factors.
  Mol Cell Biol, 28, 1883-1891.  
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
17697097 F.Werner (2007).
Structure and function of archaeal RNA polymerases.
  Mol Microbiol, 65, 1395-1404.  
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
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.  
17201921 K.B.Sheehan, K.McInnerney, B.Purevdorj-Gage, S.D.Altenburg, and L.E.Hyman (2007).
Yeast genomic expression patterns in response to low-shear modeled microgravity.
  BMC Genomics, 8, 3.  
17937913 K.Lorenzen, A.Vannini, P.Cramer, and A.J.Heck (2007).
Structural biology of RNA polymerase III: mass spectrometry elucidates subcomplex architecture.
  Structure, 15, 1237-1245.  
17676030 P.Cramer (2007).
Finding the right spot to start transcription.
  Nat Struct Mol Biol, 14, 686-687.  
17536176 P.Sadhale, J.Verma, and A.Naorem (2007).
Basal transcription machinery: role in regulation of stress response in eukaryotes.
  J Biosci, 32, 569-578.  
17875743 R.Lotan, V.Goler-Baron, L.Duek, G.Haimovich, and M.Choder (2007).
The Rpb7p subunit of yeast RNA polymerase II plays roles in the two major cytoplasmic mRNA decay mechanisms.
  J Cell Biol, 178, 1133-1143.  
16818233 A.J.Jasiak, K.J.Armache, B.Martens, R.P.Jansen, and P.Cramer (2006).
Structural biology of RNA polymerase III: subcomplex C17/25 X-ray structure and 11 subunit enzyme model.
  Mol Cell, 23, 71-81.
PDB code: 2ckz
16327806 A.Ujvári, and D.S.Luse (2006).
RNA emerging from the active site of RNA polymerase II interacts with the Rpb7 subunit.
  Nat Struct Mol Biol, 13, 49-54.  
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.  
16877568 G.M.Proshkina, E.K.Shematorova, S.A.Proshkin, C.Zaros, P.Thuriaux, and G.V.Shpakovski (2006).
Ancient origin, functional conservation and fast evolution of DNA-dependent RNA polymerase III.
  Nucleic Acids Res, 34, 3615-3624.  
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.  
16964259 L.Larivière, S.Geiger, S.Hoeppner, S.Röther, K.Strässer, and P.Cramer (2006).
Structure and TBP binding of the Mediator head subcomplex Med8-Med18-Med20.
  Nat Struct Mol Biol, 13, 895-901.
PDB codes: 2hzm 2hzs
16826228 M.Hampsey (2006).
The Pol II initiation complex: finding a place to start.
  Nat Struct Mol Biol, 13, 564-566.  
17056745 M.Selitrennik, L.Duek, R.Lotan, and M.Choder (2006).
Nucleocytoplasmic shuttling of the Rpb4p and Rpb7p subunits of Saccharomyces cerevisiae RNA polymerase II by two pathways.
  Eukaryot Cell, 5, 2092-2103.  
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.  
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.  
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.  
16094453 B.Coulombe, and M.F.Langelier (2005).
Functional dissection of the catalytic mechanism of mammalian RNA polymerase II.
  Biochem Cell Biol, 83, 497-504.  
15612920 C.Zaros, and P.Thuriaux (2005).
Rpc25, a conserved RNA polymerase III subunit, is critical for transcription initiation.
  Mol Microbiol, 55, 104-114.  
15971229 G.Cavelier, and D.Anastassiou (2005).
Phenotype analysis using network motifs derived from changes in regulatory network dynamics.
  Proteins, 60, 525-546.  
16282592 H.Meka, F.Werner, S.C.Cordell, S.Onesti, and P.Brick (2005).
Crystal structure and RNA binding of the Rpb4/Rpb7 subunits of human RNA polymerase II.
  Nucleic Acids Res, 33, 6435-6444.
PDB code: 2c35
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.  
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.  
15886393 M.F.Langelier, D.Baali, V.Trinh, J.Greenblatt, J.Archambault, and B.Coulombe (2005).
The highly conserved glutamic acid 791 of Rpb2 is involved in the binding of NTP and Mg(B) in the active center of human RNA polymerase II.
  Nucleic Acids Res, 33, 2629-2639.  
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.  
16357218 R.Lotan, V.G.Bar-On, L.Harel-Sharvit, L.Duek, D.Melamed, and M.Choder (2005).
The RNA polymerase II subunit Rpb4p mediates decay of a specific class of mRNAs.
  Genes Dev, 19, 3004-3016.  
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
15241417 A.Meinhart, and P.Cramer (2004).
Recognition of RNA polymerase II carboxy-terminal domain by 3'-RNA-processing factors.
  Nature, 430, 223-226.
PDB codes: 1sz9 1sza
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.  
15003120 C.Brochier, P.Forterre, and S.Gribaldo (2004).
Archaeal phylogeny based on proteins of the transcription and translation machineries: tackling the Methanopyrus kandleri paradox.
  Genome Biol, 5, R17.  
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.  
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.  
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.  
14704357 S.R.Singh, N.Rekha, B.Pillai, V.Singh, A.Naorem, V.Sampath, N.Srinivasan, and P.P.Sadhale (2004).
Domainal organization of the lower eukaryotic homologs of the yeast RNA polymerase II core subunit Rpb7 reflects functional conservation.
  Nucleic Acids Res, 32, 201-210.  
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.  
12782794 F.J.Asturias, and J.L.Craighead (2003).
RNA polymerase II at initiation.
  Proc Natl Acad Sci U S A, 100, 6893-6895.  
12914699 H.Kettenberger, K.J.Armache, and P.Cramer (2003).
Architecture of the RNA polymerase II-TFIIS complex and implications for mRNA cleavage.
  Cell, 114, 347-357.
PDB code: 1pqv
12907709 H.Mitsuzawa, E.Kanda, and A.Ishihama (2003).
Rpb7 subunit of RNA polymerase II interacts with an RNA-binding protein involved in processing of transcripts.
  Nucleic Acids Res, 31, 4696-4701.  
14536083 H.T.Chen, and S.Hahn (2003).
Binding of TFIIB to RNA polymerase II: Mapping the binding site for the TFIIB zinc ribbon domain within the preinitiation complex.
  Mol Cell, 12, 437-447.  
14550628 K.M.Arndt, and C.M.Kane (2003).
Running with RNA polymerase: eukaryotic transcript elongation.
  Trends Genet, 19, 543-550.  
12942140 S.Buratowski (2003).
The CTD code.
  Nat Struct Biol, 10, 679-680.  
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.  
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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