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PDBsum entry 3k1f

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protein metals Protein-protein interface(s) links
Transcription PDB id
3k1f
Jmol
Contents
Protein chains
1416 a.a. *
1120 a.a. *
266 a.a. *
178 a.a. *
214 a.a. *
87 a.a. *
171 a.a. *
134 a.a. *
119 a.a. *
65 a.a. *
114 a.a. *
46 a.a. *
185 a.a. *
Metals
_ZN ×9
* Residue conservation analysis
PDB id:
3k1f
Name: Transcription
Title: Crystal structure of RNA polymerase ii in complex with tfiib
Structure: DNA-directed RNA polymerase ii subunit rpb1. Chain: a. Synonym: RNA polymerase ii subunit b1, RNA polymerase ii su DNA-directed RNA polymerase iii largest subunit, RNA polyme subunit b220. DNA-directed RNA polymerase ii subunit rpb2. Chain: b. Synonym: RNA polymerase ii subunit 2, DNA-directed RNA poly 140 kda polypeptide, b150.
Source: Saccharomyces cerevisiae. Yeast. Organism_taxid: 4932. Organism_taxid: 4932
Resolution:
4.30Å     R-factor:   0.221     R-free:   0.255
Authors: D.Kostrewa,M.E.Zeller,K.-J.Armache,M.Seizl,K.Leike,M.Thomm,P
Key ref:
D.Kostrewa et al. (2009). RNA polymerase II-TFIIB structure and mechanism of transcription initiation. Nature, 462, 323-330. PubMed id: 19820686 DOI: 10.1038/nature08548
Date:
27-Sep-09     Release date:   10-Nov-09    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P04050  (RPB1_YEAST) -  DNA-directed RNA polymerase II subunit RPB1
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1733 a.a.
1416 a.a.
Protein chain
Pfam   ArchSchema ?
P08518  (RPB2_YEAST) -  DNA-directed RNA polymerase II subunit RPB2
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1224 a.a.
1120 a.a.
Protein chain
Pfam   ArchSchema ?
P16370  (RPB3_YEAST) -  DNA-directed RNA polymerase II subunit RPB3
Seq:
Struc:
318 a.a.
266 a.a.
Protein chain
Pfam   ArchSchema ?
P20433  (RPB4_YEAST) -  DNA-directed RNA polymerase II subunit RPB4
Seq:
Struc:
221 a.a.
178 a.a.
Protein chain
Pfam   ArchSchema ?
P20434  (RPAB1_YEAST) -  DNA-directed RNA polymerases I, II, and III subunit RPABC1
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
Seq:
Struc:
155 a.a.
87 a.a.
Protein chain
Pfam   ArchSchema ?
P34087  (RPB7_YEAST) -  DNA-directed RNA polymerase II subunit RPB7
Seq:
Struc:
171 a.a.
171 a.a.
Protein chain
Pfam   ArchSchema ?
P20436  (RPAB3_YEAST) -  DNA-directed RNA polymerases I, II, and III subunit RPABC3
Seq:
Struc:
146 a.a.
134 a.a.
Protein chain
Pfam   ArchSchema ?
P27999  (RPB9_YEAST) -  DNA-directed RNA polymerase II subunit RPB9
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
Seq:
Struc:
70 a.a.
65 a.a.
Protein chain
Pfam   ArchSchema ?
P38902  (RPB11_YEAST) -  DNA-directed RNA polymerase II subunit RPB11
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
Seq:
Struc:
70 a.a.
46 a.a.
Protein chain
Pfam   ArchSchema ?
P29055  (TF2B_YEAST) -  Transcription initiation factor IIB
Seq:
Struc:
345 a.a.
185 a.a.*
Key:    PfamA domain  Secondary structure
* PDB and UniProt seqs differ at 129 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains A, B: E.C.2.7.7.6  - 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   24 terms 
  Biochemical function     RNA polymerase II activity     20 terms  

 

 
    reference    
 
 
DOI no: 10.1038/nature08548 Nature 462:323-330 (2009)
PubMed id: 19820686  
 
 
RNA polymerase II-TFIIB structure and mechanism of transcription initiation.
D.Kostrewa, M.E.Zeller, K.J.Armache, M.Seizl, K.Leike, M.Thomm, P.Cramer.
 
  ABSTRACT  
 
To initiate gene transcription, RNA polymerase II (Pol II) requires the transcription factor IIB (B). Here we present the crystal structure of the complete Pol II-B complex at 4.3 A resolution, and complementary functional data. The results indicate the mechanism of transcription initiation, including the transition to RNA elongation. Promoter DNA is positioned over the Pol II active centre cleft with the 'B-core' domain that binds the wall at the end of the cleft. DNA is then opened with the help of the 'B-linker' that binds the Pol II rudder and clamp coiled-coil at the edge of the cleft. The DNA template strand slips into the cleft and is scanned for the transcription start site with the help of the 'B-reader' that approaches the active site. Synthesis of the RNA chain and rewinding of upstream DNA displace the B-reader and B-linker, respectively, to trigger B release and elongation complex formation.
 
  Selected figure(s)  
 
Figure 1.
Figure 1: Structure of Pol II–B complex. a, B domain organization and sequence conservation in the region connecting the B-ribbon and B-core. Yellow and green highlighting indicates conserved and invariant residues, respectively, between yeast (S. cerevisiae), human (Homo sapiens) and the archaeon P. furiosus (Pfu). b, Ribbon model of B as observed in its complex with Pol II. A peak in the anomalous difference Fourier (magenta) defines the zinc ion position (cyan sphere) in the B-ribbon. The view is from the side. c, Overview of the Pol II–B structure. Ribbon model with Pol II in silver and B in colours as in a. Side and front views are used. Pol II domains that interact with B are highlighted (dock, wheat; wall, blue; flap loop, light blue; clamp with coiled-coil, red; rudder, salmon; lid, dark red). The left view is from the side and lacks most of Rpb2, including the protrusion. The right view is from the front and includes Rpb2.
Figure 2.
Figure 2: Models of closed and open complexes. a, Model of the closed complex (minimal PIC). DNA template and non-template strands are in blue and cyan, respectively. The TATA element is in black and the nucleotide in the template strand that represents position +1 in the open complex is shown as a space-filling model. Top and bottom views are from the side and front, respectively. b, Model of the open complex. c, Location of nucleotides in DNA template strand initiator consensus sequence and mutations influencing start site selection and DNA opening. The open complex model is shown around the active centre. Positions -8 and +1 of the template strand are labelled. Position -8 lies adjacent to the B-reader helix that contains residues important for TSS selection (Glu 62, Trp 63, Arg 64, Phe 66, pale green spheres). The mobile B-reader loop (green-yellow), which contains residues Arg 78 and Val 79 required for initial transcription and TSS selection, could reach near positions -1 and +1. Sites of mutations abolishing DNA opening in archaeal transcription are shown as salmon spheres.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2009, 462, 323-330) 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
22258509 H.S.Rhee, and B.F.Pugh (2012).
Genome-wide structure and organization of eukaryotic pre-initiation complexes.
  Nature, 483, 295-301.  
22864359 M.Carey (2012).
PICking apart Pol II initiation.
  Nat Struct Mol Biol, 19, 737-738.  
22751016 S.Grünberg, L.Warfield, and S.Hahn (2012).
Architecture of the RNA polymerase II preinitiation complex and mechanism of ATP-dependent promoter opening.
  Nat Struct Mol Biol, 19, 788-796.  
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.  
21187417 B.J.Klein, D.Bose, K.J.Baker, Z.M.Yusoff, X.Zhang, and K.S.Murakami (2011).
RNA polymerase and transcription elongation factor Spt4/5 complex structure.
  Proc Natl Acad Sci U S A, 108, 546-550.
PDB code: 3p8b
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.  
21378965 E.Vojnic, A.Mourão, M.Seizl, B.Simon, L.Wenzeck, L.Larivière, S.Baumli, K.Baumgart, M.Meisterernst, M.Sattler, and P.Cramer (2011).
Structure and VP16 binding of the Mediator Med25 activator interaction domain.
  Nat Struct Mol Biol, 18, 404-409.
PDB code: 2xnf
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.  
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
21734658 P.Wollmann, S.Cui, R.Viswanathan, O.Berninghausen, M.N.Wells, M.Moldt, G.Witte, A.Butryn, P.Wendler, R.Beckmann, D.T.Auble, and K.P.Hopfner (2011).
Structure and mechanism of the Swi2/Snf2 remodeller Mot1 in complex with its substrate TBP.
  Nature, 475, 403-407.
PDB codes: 3oc3 3oci
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.  
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.  
21358628 S.Lefèvre, H.Dumay-Odelot, L.El-Ayoubi, A.Budd, P.Legrand, N.Pinaud, M.Teichmann, and S.Fribourg (2011).
Structure-function analysis of hRPC62 provides insights into RNA polymerase III transcription initiation.
  Nat Struct Mol Biol, 18, 352-358.
PDB codes: 2xub 2xv4
20818391 A.Mayer, M.Lidschreiber, M.Siebert, K.Leike, J.Söding, and P.Cramer (2010).
Uniform transitions of the general RNA polymerase II transcription complex.
  Nat Struct Mol Biol, 17, 1272-1278.  
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.  
  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.  
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.  
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.  
20439713 P.C.Burrows, N.Joly, and M.Buck (2010).
A prehydrolysis state of an AAA+ ATPase supports transcription activation of an enhancer-dependent RNA polymerase.
  Proc Natl Acad Sci U S A, 107, 9376-9381.  
20482321 P.Cramer (2010).
Towards molecular systems biology of gene transcription and regulation.
  Biol Chem, 391, 731-735.  
20071370 S.Wang, J.R.Shepard, and H.Shi (2010).
An RNA-based transcription activator derived from an inhibitory aptamer.
  Nucleic Acids Res, 38, 2378-2386.  
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.  
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.  
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.  
19924201 S.Hahn (2009).
Structural biology: New beginnings for transcription.
  Nature, 462, 292-293.  
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.