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PDBsum entry 3k7a
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protein metals Protein-protein interface(s) links
Transcription PDB id
3k7a

 

 

 

 

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Contents
Protein chains
1408 a.a. *
1122 a.a. *
266 a.a. *
214 a.a. *
84 a.a. *
133 a.a. *
118 a.a. *
65 a.a. *
114 a.a. *
46 a.a. *
187 a.a. *
Metals
_ZN ×9
* Residue conservation analysis
PDB id:
3k7a
Name: Transcription
Title: Crystal structure of an RNA polymerase ii-tfiib complex
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. Engineered: yes. DNA-directed RNA polymerase ii subunit rpb2. Chain: b. Synonym: RNA polymerase ii subunit 2, DNA-directed RNA polymerase ii
Source: Saccharomyces cerevisiae. Yeast. Organism_taxid: 4932. Gene: d2150, rpb1, rpb220, rpo21, sua8, ydl140c. Expressed in: saccharomyces cerevisiae. Expression_system_taxid: 4932. Gene: rpb150, rpb2, rpo22, yor151c. Gene: rpb3, yil021w. Gene: rpa7, rpb5, rpc9, ybr1204, ybr154c.
Resolution:
3.80Å     R-factor:   0.268     R-free:   0.313
Authors: X.Liu,D.A.Bushnell,D.Wang,G.Calero,R.D.Kornberg
Key ref:
X.Liu et al. (2010). Structure of an RNA polymerase II-TFIIB complex and the transcription initiation mechanism. Science, 327, 206-209. PubMed id: 19965383 DOI: 10.1126/science.1182015
Date:
12-Oct-09     Release date:   24-Nov-09    
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.
1408 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.
1122 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 ?
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 ?
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.
118 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.
Protein chain
Pfam   ArchSchema ?
P29055  (TF2B_YEAST) -  Transcription initiation factor IIB from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		345 a.a.
187 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains A, B: 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: 10.1126/science.1182015 Science 327:206-209 (2010)
PubMed id: 19965383  
 
 
Structure of an RNA polymerase II-TFIIB complex and the transcription initiation mechanism.
X.Liu, D.A.Bushnell, D.Wang, G.Calero, R.D.Kornberg.
 
  ABSTRACT  
 
Previous x-ray crystal structures have given insight into the mechanism of transcription and the role of general transcription factors in the initiation of the process. A structure of an RNA polymerase II-general transcription factor TFIIB complex at 4.5 angstrom resolution revealed the amino-terminal region of TFIIB, including a loop termed the "B finger," reaching into the active center of the polymerase where it may interact with both DNA and RNA, but this structure showed little of the carboxyl-terminal region. A new crystal structure of the same complex at 3.8 angstrom resolution obtained under different solution conditions is complementary with the previous one, revealing the carboxyl-terminal region of TFIIB, located above the polymerase active center cleft, but showing none of the B finger. In the new structure, the linker between the amino- and carboxyl-terminal regions can also be seen, snaking down from above the cleft toward the active center. The two structures, taken together with others previously obtained, dispel long-standing mysteries of the transcription initiation process.
 
  Selected figure(s)  
 
Figure 1.
Structure of pol II TFIIB complex. (A) "Top" view of pol II in a surface representation, with previously identified domains in the colors indicated, and with TFIIB in ribbon representation. TFIIB zinc ribbon (TFIIB[N]), linker (TFIIB[L]), first cyclin repeat (TFIIB[C]) are indicated. (B) Difference (F[o]-F[c]) electron density map between pol II TFIIB and pol II alone, contoured at 2.0[sigma], shown in green mesh, and Se-Met anomalous peaks, contoured at 6-10[sigma], shown in blue mesh. Science. Author manuscript; available in PMC 2010 January 28. Published in final edited form as: Science. 2010 January 8; 327(5962): 206. Published online 2009 November 12. doi: 10.1126/science.1182015. Copyright notice and Disclaimer
Figure 3.
Comparison of TFIIB and bacterial [sigma] factor structures. (A) Superposition of TFIIB (red) and [sigma] factor (green) structures. Conserved residues H455 and E458 of [sigma] factors that bind to the -10 element and mark the start of transcription bubble formation are highlighted as blue spheres. Corresponding domains from TFIIB and [sigma] factor are labeled. (B) Same as (A) rotated 45[deg] around the X-axis. The B-finger (TFIIB[F]) from the previous cocrystal structure is shown as a dashed black line. Science. Author manuscript; available in PMC 2010 January 28. Published in final edited form as: Science. 2010 January 8; 327(5962): 206. Published online 2009 November 12. doi: 10.1126/science.1182015. Copyright notice and Disclaimer
 
  The above figures are reprinted from an Open Access publication published by the AAAs: Science (2010, 327, 206-209) copyright 2010.  
  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.  
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
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.  
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.  
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.  
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.  
  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.  
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.  
20226668 Y.Wang, J.A.Fairley, and S.G.Roberts (2010).
Phosphorylation of TFIIB links transcription initiation and termination.
  Curr Biol, 20, 548-553.  
  21326885 Y.Wang, and S.G.Roberts (2010).
New insights into the role of TFIIB in transcription initiation.
  Transcr, 1, 126-129.  
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.

 

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