PDBsum entry 3hoy

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protein dna_rna metals Protein-protein interface(s) links
Transcription,transferase/DNA/RNA hybrid PDB id
Protein chains
1419 a.a. *
1105 a.a. *
266 a.a. *
178 a.a. *
213 a.a. *
87 a.a. *
171 a.a. *
133 a.a. *
119 a.a. *
65 a.a. *
114 a.a. *
46 a.a. *
_ZN ×8
* Residue conservation analysis
PDB id:
Name: Transcription,transferase/DNA/RNA hybrid
Title: Complete RNA polymerase ii elongation complex vi
Structure: DNA-directed RNA polymerase ii subunit rpb1. Chain: a. Synonym: RNA polymerase ii subunit b1, RNA polymerase ii subunit 1, DNA-directed RNA polymerase iii largest subunit, RNA polymerase ii subunit b220. DNA-directed RNA polymerase ii subunit rpb2. Chain: b. Synonym: RNA polymerase ii subunit 2, DNA-directed RNA polymerase ii 140 kda polypeptide, b150.
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Synthetic: yes. Synthetic: yes
3.40Å     R-factor:   0.216     R-free:   0.254
Authors: J.F.Sydow,F.Brueckner,A.C.M.Cheung,G.E.Damsma,S.Dengl, E.Lehmann,D.Vassylyev,P.Cramer
Key ref:
J.F.Sydow et al. (2009). Structural basis of transcription: mismatch-specific fidelity mechanisms and paused RNA polymerase II with frayed RNA. Mol Cell, 34, 710-721. PubMed id: 19560423 DOI: 10.1016/j.molcel.2009.06.002
03-Jun-09     Release date:   28-Jul-09    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P04050  (RPB1_YEAST) -  DNA-directed RNA polymerase II subunit RPB1
1733 a.a.
1419 a.a.
Protein chain
Pfam   ArchSchema ?
P08518  (RPB2_YEAST) -  DNA-directed RNA polymerase II subunit RPB2
1224 a.a.
1105 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.
178 a.a.
Protein chain
Pfam   ArchSchema ?
P20434  (RPAB1_YEAST) -  DNA-directed RNA polymerases I, II, and III subunit RPABC1
215 a.a.
213 a.a.
Protein chain
Pfam   ArchSchema ?
P20435  (RPAB2_YEAST) -  DNA-directed RNA polymerases I, II, and III subunit RPABC2
155 a.a.
87 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.
114 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   22 terms 
  Biochemical function     RNA polymerase II activity     19 terms  


DOI no: 10.1016/j.molcel.2009.06.002 Mol Cell 34:710-721 (2009)
PubMed id: 19560423  
Structural basis of transcription: mismatch-specific fidelity mechanisms and paused RNA polymerase II with frayed RNA.
J.F.Sydow, F.Brueckner, A.C.Cheung, G.E.Damsma, S.Dengl, E.Lehmann, D.Vassylyev, P.Cramer.
We show that RNA polymerase (Pol) II prevents erroneous transcription in vitro with different strategies that depend on the type of DNARNA base mismatch. Certain mismatches are efficiently formed but impair RNA extension. Other mismatches allow for RNA extension but are inefficiently formed and efficiently proofread by RNA cleavage. X-ray analysis reveals that a TU mismatch impairs RNA extension by forming a wobble base pair at the Pol II active center that dissociates the catalytic metal ion and misaligns the RNA 3' end. The mismatch can also stabilize a paused state of Pol II with a frayed RNA 3' nucleotide. The frayed nucleotide binds in the Pol II pore either parallel or perpendicular to the DNA-RNA hybrid axis (fraying sites I and II, respectively) and overlaps the nucleoside triphosphate (NTP) site, explaining how it halts transcription during proofreading, before backtracking and RNA cleavage.
  Selected figure(s)  
Figure 5.
Figure 5. Frayed Nucleotides Overlap the NTP, Closed Trigger Loop, and the TFIIS Hairpin
(A) Frayed nucleotides overlap the NTP bound to the insertion site (green cyan, taken from bacterial Pol EC, PDB-code 2O5J [Vassylyev et al., 2007b]). Van der Waals radii are represented by colored dots. All structures were superimposed with their active site regions.
(B and C) Frayed nucleotides overlap the closed trigger loop (cyan) at residue F1084 (B, taken from the Pol II EC, PDB-code 2E2H [Wang et al., 2006]) and/or at residue H1242 (C, bacterial Pol EC, PDB-code 2O5J [Vassylyev et al., 2007b]).
(D) Frayed nucleotides overlap the tip of the hairpin of the cleavage-stimulatory factor TFIIS. The structures of EC III, EC IV, and the Pol II-TFIIS complex (PDB-code 1PQV, [Kettenberger et al., 2003]) were superimposed with their active center regions. TFIIS is shown in orange. The canonical side view is used.
(E) Detailed view of the superposition in (D) around the active site, revealing a potential clash of the TFIIS acidic hairpin with the frayed nucleotides.
Figure 6.
Figure 6. Fork Loop 2-Downstream DNA Contact
(A) Comparison of the conformation of fork loop 2 in EC III with that in previous Pol II EC structures (PDB-codes 1Y1W (Kettenberger et al., 2004) and 2E2I (Wang et al., 2006).
(B) Interaction of the side chain of fork loop 2 Rpb2 residue R504 with the guanine base at position +4 of downstream DNA. The final 2F[o]-F[c] electron density is shown in blue, contoured at 0.7 σ.
(C) Interaction of regions in EC III that may be involved in pausing, including the frayed nucleotide, βDloopII, the bridge helix, fork loop 2, and downstream DNA.
(D) Multiple sequence alignment of fork loop 2 and surrounding Rpb2 residues from S. cerevisiae, H. sapiens, P. furiosus, E. coli, and T. thermophilus (CLUSTAL W). The conserved R504 from S. cerevisiae is highlighted in blue.
  The above figures are reprinted by permission from Cell Press: Mol Cell (2009, 34, 710-721) copyright 2009.  
  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
21346759 A.C.Cheung, and P.Cramer (2011).
Structural basis of RNA polymerase II backtracking, arrest and reactivation.
  Nature, 471, 249-253.
PDB codes: 3po2 3po3
21206491 C.Miller, B.Schwalb, K.Maier, D.Schulz, S.Dümcke, B.Zacher, A.Mayer, J.Sydow, L.Marcinowski, L.Dölken, D.E.Martin, A.Tresch, and P.Cramer (2011).
Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast.
  Mol Syst Biol, 7, 458.  
21504834 E.Czeko, M.Seizl, C.Augsberger, T.Mielke, and P.Cramer (2011).
Iwr1 directs RNA polymerase II nuclear import.
  Mol Cell, 42, 261-266.  
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
21292158 M.H.Larson, R.Landick, and S.M.Block (2011).
Single-molecule studies of RNA polymerase: one singular sensation, every little step it takes.
  Mol Cell, 41, 249-262.  
21447716 S.R.Kennedy, and D.A.Erie (2011).
Templated nucleoside triphosphate binding to a noncatalytic site on RNA polymerase regulates transcription.
  Proc Natl Acad Sci U S A, 108, 6079-6084.  
21478900 T.J.Santangelo, and I.Artsimovitch (2011).
Termination and antitermination: RNA polymerase runs a stop sign.
  Nat Rev Microbiol, 9, 319-329.  
20639538 A.Sevostyanova, and I.Artsimovitch (2010).
Functional analysis of Thermus thermophilus transcription factor NusG.
  Nucleic Acids Res, 38, 7432-7445.  
20132437 G.A.Belogurov, A.Sevostyanova, V.Svetlov, and I.Artsimovitch (2010).
Functional regions of the N-terminal domain of the antiterminator RfaH.
  Mol Microbiol, 76, 286-301.  
19940126 G.A.Kassavetis, P.Prakash, and E.Shim (2010).
The C53/C37 subcomplex of RNA polymerase III lies near the active site and participates in promoter opening.
  J Biol Chem, 285, 2695-2706.  
20088966 H.Koyama, T.Ueda, T.Ito, and K.Sekimizu (2010).
Novel RNA polymerase II mutation suppresses transcriptional fidelity and oxidative stress sensitivity in rpb9Delta yeast.
  Genes Cells, 15, 151-159.  
19966797 J.Zhang, M.Palangat, and R.Landick (2010).
Role of the RNA polymerase trigger loop in catalysis and pausing.
  Nat Struct Mol Biol, 17, 99.  
20367031 L.A.Selth, S.Sigurdsson, and J.Q.Svejstrup (2010).
Transcript Elongation by RNA Polymerase II.
  Annu Rev Biochem, 79, 271-293.  
20482321 P.Cramer (2010).
Towards molecular systems biology of gene transcription and regulation.
  Biol Chem, 391, 731-735.  
20398323 Q.Gan, D.E.Schones, S.Ho Eun, G.Wei, K.Cui, K.Zhao, and X.Chen (2010).
Monovalent and unpoised status of most genes in undifferentiated cell-enriched Drosophila testis.
  Genome Biol, 11, R42.  
21124318 S.Tagami, S.Sekine, T.Kumarevel, N.Hino, Y.Murayama, S.Kamegamori, M.Yamamoto, K.Sakamoto, and S.Yokoyama (2010).
Crystal structure of bacterial RNA polymerase bound with a transcription inhibitor protein.
  Nature, 468, 978-982.
PDB codes: 3aoh 3aoi
20459653 Y.Yuzenkova, A.Bochkareva, V.R.Tadigotla, M.Roghanian, S.Zorov, K.Severinov, and N.Zenkin (2010).
Stepwise mechanism for transcription fidelity.
  BMC Biol, 8, 54.  
20094031 Z.A.Chen, A.Jawhari, L.Fischer, C.Buchen, S.Tahir, T.Kamenski, M.Rasmussen, L.Lariviere, J.C.Bukowski-Wills, M.Nilges, P.Cramer, and J.Rappsilber (2010).
Architecture of the RNA polymerase II-TFIIF complex revealed by cross-linking and mass spectrometry.
  EMBO J, 29, 717-726.  
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
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
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.