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PDBsum entry 1nik
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protein metals Protein-protein interface(s) links
Transcription PDB id
1nik
Contents
Protein chains
1388 a.a. *
1097 a.a. *
266 a.a. *
153 a.a.* *
214 a.a. *
84 a.a. *
170 a.a.* *
133 a.a. *
119 a.a. *
65 a.a. *
114 a.a. *
46 a.a. *
Metals
_ZN ×7
* Residue conservation analysis
* C-alpha coords only
PDB id:
1nik
Name: Transcription
Title: Wild type RNA polymerase ii
Structure: Rpb1. Chain: a. Synonym: DNA-directed RNA polymerase ii largest subunit. Orf yor151c. Chain: b. Synonym: RNA polymerase ii subunit 2. DNA-directed RNA polymerase ii, chain rpb3. Chain: c. DNA-directed RNA polymerase ii, chain rpb4.
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Organism_taxid: 4932
Biol. unit: Dodecamer (from PQS)
Resolution:
4.10Å     R-factor:   0.334     R-free:   0.360
Authors: D.A.Bushnell,R.D.Kornberg
Key ref:
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. PubMed id: 12746498 DOI: 10.1073/pnas.1130601100
Date:
24-Dec-02     Release date:   29-Apr-03    
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.
1388 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
No UniProt id for this chain
Struc: 153 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
No UniProt id for this chain
Struc: 170 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

 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: 10.1073/pnas.1130601100 Proc Natl Acad Sci U S A 100:6969-6973 (2003)
PubMed id: 12746498  
 
 
Complete, 12-subunit RNA polymerase II at 4.1-A resolution: implications for the initiation of transcription.
D.A.Bushnell, R.D.Kornberg.
 
  ABSTRACT  
 
The x-ray structure of complete RNA polymerase II from Saccharomyces cerevisiae has been determined, including a heterodimer of subunits Rpb4 and Rpb7 not present in previous "core" polymerase II structures. The heterodimer maintains the polymerase in the conformation of a transcribing complex, may bind RNA as it emerges from the enzyme, and is in a position to interact with general transcription factors and the Mediator of transcriptional regulation.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. Backbone model of complete, 12-subunit pol II. Shown is a ribbon representation of the complete pol II structure (top and back views as in refs. 10 and 11). Rpb1 is gray, Rpb2 is bronze, Rpb4 is red, Rpb6 is green, the N-terminal half of Rpb7 that contains the RNP domain is dark blue, the C-terminal half of Rpb7 that contains the OB fold is light blue, and the remaining subunits are black. The locations of the clamp, the C-terminal repeat domain (CTD), and the previously proposed RNA exit groove 1 (pink dashed line) are indicated. The figure was generated with SWISS-PDB VIEWER and POV-RAY (40). 		Figure 3.
Fig. 3. Relationship of complete pol II x-ray structure to EM structures of complete pol II (A) and Mediator-pol II complex (B). As this complex was prepared from exponentially growing yeast, it would have been largely deficient in Rpb4/Rpb7, accounting for the lack of density in this region of the EM map. The core pol II model is blue in A and yellow in B. Rpb4 is red and Rpb7 is dark blue. The figure was generated by using O and POV-RAY (19).
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21468301 C.Bernecky, P.Grob, C.C.Ebmeier, E.Nogales, and D.J.Taatjes (2011).
Molecular architecture of the human Mediator-RNA polymerase II-TFIIF assembly.
  PLoS Biol, 9, e1000603.
PDB code: 3j0k
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.  
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.  
20042611 B.Ding, D.LeJeune, and S.Li (2010).
The C-terminal repeat domain of Spt5 plays an important role in suppression of Rad26-independent transcription coupled repair.
  J Biol Chem, 285, 5317-5326.  
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.  
21217813 N.Corbi, E.M.Batassa, C.Pisani, A.Onori, M.G.Di Certo, G.Strimpakos, M.Fanciulli, E.Mattei, and C.Passananti (2010).
The eEF1γ subunit contacts RNA polymerase II and binds vimentin promoter region.
  PLoS One, 5, e14481.  
20505070 S.L.Schmid, and M.G.Farquhar (2010).
The Palade symposium: celebrating cell biology at its best.
  Mol Biol Cell, 21, 2367-2370.  
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.  
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.  
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.  
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
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.  
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
18607770 R.Todorova (2009).
In vitro interaction between the N-terminus of the Ewing's sarcoma protein and the subunit of RNA polymerase II hsRPB7.
  Mol Biol Rep, 36, 1269-1274.  
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.  
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
17951525 A.Das, M.Banday, and V.Bellofatto (2008).
RNA polymerase transcription machinery in trypanosomes.
  Eukaryot Cell, 7, 429-434.  
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.  
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.  
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.  
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.  
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.  
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.  
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.  
16980443 N.W.Goehring, I.Petrovska, D.Boyd, and J.Beckwith (2007).
Mutants, suppressors, and wrinkled colonies: mutant alleles of the cell division gene ftsQ point to functional domains in FtsQ and a role for domain 1C of FtsA in divisome assembly.
  J Bacteriol, 189, 633-645.  
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.  
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.  
16818233 A.J.Jasiak, K.J.Armache, B.Martens, R.P.Jansen, and P.Cramer (2006).
Structural biology of RNA polymerase III: subcomplex C17/25 X-ray structure and 11 subunit enzyme model.
  Mol Cell, 23, 71-81.
PDB code: 2ckz
16327806 A.Ujvári, and D.S.Luse (2006).
RNA emerging from the active site of RNA polymerase II interacts with the Rpb7 subunit.
  Nat Struct Mol Biol, 13, 49-54.  
17381329 C.S.Pikaard (2006).
Cell biology of the Arabidopsis nuclear siRNA pathway for RNA-directed chromatin modification.
  Cold Spring Harb Symp Quant Biol, 71, 473-480.  
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.  
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.  
16729021 H.Hernández, A.Dziembowski, T.Taverner, B.Séraphin, and C.V.Robinson (2006).
Subunit architecture of multimeric complexes isolated directly from cells.
  EMBO Rep, 7, 605-610.  
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
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.  
16972065 N.Sharma, S.Marguerat, S.Mehta, S.Watt, and J.Bähler (2006).
The fission yeast Rpb4 subunit of RNA polymerase II plays a specialized role in cell separation.
  Mol Genet Genomics, 276, 545-554.  
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.  
16406702 R.Peters (2006).
Checking and fixing the cellular nanomachinery: towards medical nanoscopy.
  Trends Mol Med, 12, 83-89.  
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.  
16769904 X.Hu, S.Malik, C.C.Negroiu, K.Hubbard, C.N.Velalar, B.Hampton, D.Grosu, J.Catalano, R.G.Roeder, and A.Gnatt (2006).
A Mediator-responsive form of metazoan RNA polymerase II.
  Proc Natl Acad Sci U S A, 103, 9506-9511.  
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.  
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.  
15998810 Z.Zhang, J.Fu, and D.S.Gilmour (2005).
CTD-dependent dismantling of the RNA polymerase II elongation complex by the pre-mRNA 3'-end processing factor, Pcf11.
  Genes Dev, 19, 1572-1580.  
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.  
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.  
15254252 F.Zhang, L.Sumibcay, A.G.Hinnebusch, and M.J.Swanson (2004).
A triad of subunits from the Gal11/tail domain of Srb mediator is an in vivo target of transcriptional activator Gcn4p.
  Mol Cell Biol, 24, 6871-6886.  
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.  
15281131 V.Anantharaman, and L.Aravind (2004).
The SHS2 module is a common structural theme in functionally diverse protein groups, like Rpb7p, FtsA, GyrI, and MTH1598/TM1083 superfamilies.
  Proteins, 56, 795-807.  
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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