PDBsum entry 1wcm

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protein metals Protein-protein interface(s) links
Transcription PDB id
Protein chains
1416 a.a. *
1097 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. *
115 a.a. *
46 a.a. *
_ZN ×8
* Residue conservation analysis
PDB id:
Name: Transcription
Title: Complete 12-subunit RNA polymerase ii at 3.8 ang
Structure: DNA-directed RNA polymerase ii largest subunit. Chain: a. Synonym: rpb1, b220. DNA-directed RNA polymerase ii second largest subunit. Chain: b. Synonym: rpb2, b150, DNA-directed RNA polymerase ii 140 kda polypeptide, RNA polymerase ii subunit 2. DNA-directed RNA polymerase ii 45 kda
Source: Saccharomyces cerevisiae. Yeast. Organism_taxid: 4932. Expressed in: escherichia coli. Expression_system_taxid: 469008. Organism_taxid: 4932
Biol. unit: Dodecamer (from PDB file)
3.80Å     R-factor:   0.256     R-free:   0.285
Authors: K.-J.Armache,S.Mitterweger,A.Meinhart,P.Cramer
Key ref:
K.J.Armache et al. (2005). Structures of complete RNA polymerase II and its subcomplex, Rpb4/7. J Biol Chem, 280, 7131-7134. PubMed id: 15591044 DOI: 10.1074/jbc.M413038200
17-Nov-04     Release date:   14-Dec-04    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P04050  (RPB1_YEAST) -  DNA-directed RNA polymerase II subunit RPB1
1733 a.a.
1416 a.a.
Protein chain
Pfam   ArchSchema ?
P08518  (RPB2_YEAST) -  DNA-directed RNA polymerase II subunit RPB2
1224 a.a.
1097 a.a.
Protein chain
Pfam   ArchSchema ?
P16370  (RPB3_YEAST) -  DNA-directed RNA polymerase II subunit RPB3
318 a.a.
266 a.a.
Protein chain
Pfam   ArchSchema ?
P20433  (RPB4_YEAST) -  DNA-directed RNA polymerase II subunit RPB4
221 a.a.
177 a.a.
Protein chain
Pfam   ArchSchema ?
P20434  (RPAB1_YEAST) -  DNA-directed RNA polymerases I, II, and III subunit RPABC1
215 a.a.
214 a.a.
Protein chain
Pfam   ArchSchema ?
P20435  (RPAB2_YEAST) -  DNA-directed RNA polymerases I, II, and III subunit RPABC2
155 a.a.
84 a.a.
Protein chain
Pfam   ArchSchema ?
P34087  (RPB7_YEAST) -  DNA-directed RNA polymerase II subunit RPB7
171 a.a.
171 a.a.
Protein chain
Pfam   ArchSchema ?
P20436  (RPAB3_YEAST) -  DNA-directed RNA polymerases I, II, and III subunit RPABC3
146 a.a.
133 a.a.
Protein chain
Pfam   ArchSchema ?
P27999  (RPB9_YEAST) -  DNA-directed RNA polymerase II subunit RPB9
122 a.a.
119 a.a.
Protein chain
Pfam   ArchSchema ?
P22139  (RPAB5_YEAST) -  DNA-directed RNA polymerases I, II, and III subunit RPABC5
70 a.a.
65 a.a.
Protein chain
Pfam   ArchSchema ?
P38902  (RPB11_YEAST) -  DNA-directed RNA polymerase II subunit RPB11
120 a.a.
115 a.a.
Protein chain
Pfam   ArchSchema ?
P40422  (RPAB4_YEAST) -  DNA-directed RNA polymerases I, II, and III subunit RPABC4
70 a.a.
46 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains A, B: E.C.  - DNA-directed Rna polymerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Nucleoside triphosphate
+ RNA(n)
= diphosphate
+ RNA(n+1)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   8 terms 
  Biological process     transcription, RNA-dependent   18 terms 
  Biochemical function     RNA polymerase II activity     20 terms  


DOI no: 10.1074/jbc.M413038200 J Biol Chem 280:7131-7134 (2005)
PubMed id: 15591044  
Structures of complete RNA polymerase II and its subcomplex, Rpb4/7.
K.J.Armache, S.Mitterweger, A.Meinhart, P.Cramer.
We determined the x-ray structure of the RNA polymerase (Pol) II subcomplex Rpb4/7 at 2.3 A resolution, combined it with a previous structure of the 10-subunit polymerase core, and refined an atomic model of the complete 12-subunit Pol II at 3.8-A resolution. Comparison of the complete Pol II structure with structures of the Pol II core and free Rpb4/7 shows that the core-Rpb4/7 interaction goes along with formation of an alpha-helix in the linker region of the largest Pol II subunit and with folding of the conserved Rpb7 tip loop. Details of the core-Rpb4/7 interface explain facilitated Rpb4/7 dissociation in a temperature-sensitive Pol II mutant and specific assembly of Pol I with its Rpb4/7 counterpart, A43/14. The refined atomic model of Pol II serves as the new reference structure for analysis of the transcription mechanism and enables structure solution of complexes of the complete enzyme with additional factors and nucleic acids by molecular replacement.
  Selected figure(s)  
Figure 2.
FIG. 2. Electron density maps. 2F[o] - F[c] electron density maps around the final model of Rpb4 residues 176-196 are shown for free Rpb4/7 at 2.3-Å resolution (left) and for the complete Pol II at 3.8-Å resolution (right). The maps are contoured at 1 . The figure was prepared with BOBSCRIPT (26).
Figure 4.
FIG. 4. Folding transitions upon Rpb4/7 binding to the Pol II core. The complete Pol II structure (left) and free Rpb4/7 structure (right) are represented as gray coils. Elements that fold upon the interaction are colored blue (Rpb7 tip loop), red (Rpb4 amino-terminal extension), and orange (additional helix 50 in the Rpb1 linker to the carboxyl-terminal domain).
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2005, 280, 7131-7134) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
23151482 S.Sainsbury, J.Niesser, and P.Cramer (2013).
Structure and function of the initially transcribing RNA polymerase II-TFIIB complex.
  Nature, 493, 437-440.
PDB codes: 4bbr 4bbs
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.  
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.  
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.  
21265742 M.Wojtas, B.Peralta, M.Ondiviela, M.Mogni, S.D.Bell, and N.G.Abrescia (2011).
Archaeal RNA polymerase: the influence of the protruding stalk in crystal packing and preliminary biophysical analysis of the Rpo13 subunit.
  Biochem Soc Trans, 39, 25-30.
PDB code: 2y0s
21250781 S.H.Jun, M.J.Reichlen, M.Tajiri, and K.S.Murakami (2011).
Archaeal RNA polymerase and transcription regulation.
  Crit Rev Biochem Mol Biol, 46, 27-40.  
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.  
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.  
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.  
  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.  
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.  
20797630 S.R.Geiger, K.Lorenzen, A.Schreieck, P.Hanecker, D.Kostrewa, A.J.Heck, and P.Cramer (2010).
RNA polymerase I contains a TFIIF-related DNA-binding subcomplex.
  Mol Cell, 39, 583-594.
PDB codes: 3nff 3nfg 3nfh 3nfi
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.  
19880312 A.Hirata, and K.S.Murakami (2009).
Archaeal RNA polymerase.
  Curr Opin Struct Biol, 19, 724-731.  
19492989 D.Grohmann, A.Hirtreiter, and F.Werner (2009).
RNAP subunits F/E (RPB4/7) are stably associated with archaeal RNA polymerase: using fluorescence anisotropy to monitor RNAP assembly in vitro.
  Biochem J, 421, 339-343.  
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.  
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
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
19278646 R.Landick (2009).
Functional divergence in the growing family of RNA polymerases.
  Structure, 17, 323-325.  
19110459 T.S.Ream, J.R.Haag, A.T.Wierzbicki, C.D.Nicora, A.D.Norbeck, J.K.Zhu, G.Hagen, T.J.Guilfoyle, L.Pasa-Tolić, and C.S.Pikaard (2009).
Subunit compositions of the RNA-silencing enzymes Pol IV and Pol V reveal their origins as specialized forms of RNA polymerase II.
  Mol Cell, 33, 192-203.  
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
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.  
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.  
18408053 P.A.Gibney, T.Fries, S.M.Bailer, and K.A.Morano (2008).
Rtr1 is the Saccharomyces cerevisiae homolog of a novel family of RNA polymerase II-binding proteins.
  Eukaryot Cell, 7, 938-948.  
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.  
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.  
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.  
18160037 C.D.Kuhn, S.R.Geiger, S.Baumli, M.Gartmann, J.Gerber, S.Jennebach, T.Mielke, H.Tschochner, R.Beckmann, and P.Cramer (2007).
Functional architecture of RNA polymerase I.
  Cell, 131, 1260-1272.
PDB code: 2rf4
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.  
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.  
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
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.  
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.  
17572682 Y.Wei, S.Liu, J.Lausen, C.Woodrell, S.Cho, N.Biris, N.Kobayashi, Y.Wei, S.Yokoyama, and M.H.Werner (2007).
A TAF4-homology domain from the corepressor ETO is a docking platform for positive and negative regulators of transcription.
  Nat Struct Mol Biol, 14, 653-661.
PDB code: 2pp4
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
16912294 G.Delhon, E.R.Tulman, C.L.Afonso, Z.Lu, J.J.Becnel, B.A.Moser, G.F.Kutish, and D.L.Rock (2006).
Genome of invertebrate iridescent virus type 3 (mosquito iridescent virus).
  J Virol, 80, 8439-8449.  
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.  
17043218 H.Elmlund, V.Baraznenok, M.Lindahl, C.O.Samuelsen, P.J.Koeck, S.Holmberg, H.Hebert, and C.M.Gustafsson (2006).
The cyclin-dependent kinase 8 module sterically blocks Mediator interactions with RNA polymerase II.
  Proc Natl Acad Sci U S A, 103, 15788-15793.  
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.  
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.  
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.  
15916593 E.P.Geiduschek, and M.Ouhammouch (2005).
Archaeal transcription and its regulators.
  Mol Microbiol, 56, 1397-1407.  
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
16249119 M.S.Bartlett (2005).
Determinants of transcription initiation by archaeal RNA polymerase.
  Curr Opin Microbiol, 8, 677-684.  
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.