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protein dna_rna Protein-protein interface(s) links
Transcription/DNA PDB id
1c9b
Jmol
Contents
Protein chains
207 a.a. *
180 a.a. *
DNA/RNA
Waters ×329
* Residue conservation analysis
PDB id:
1c9b
Name: Transcription/DNA
Title: Crystal structure of a human tbp core domain-human tfiib core domain complex bound to an extended, modified adenoviral major late promoter (admlp)
Structure: Admlp tata-box DNA containing iib recognition element. Chain: c, g, k, o, s. Engineered: yes. Admlp tata-box DNA containing iib recognition element. Chain: d, h, l, p, t. Engineered: yes. General transcription factor iib.
Source: Synthetic: yes. Other_details: natural sequence of adenoviral major late promoter. Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Not given
Resolution:
2.65Å     R-factor:   0.229     R-free:   0.260
Authors: F.T.F.Tsai,P.B.Sigler
Key ref:
F.T.Tsai and P.B.Sigler (2000). Structural basis of preinitiation complex assembly on human pol II promoters. EMBO J, 19, 25-36. PubMed id: 10619841 DOI: 10.1093/emboj/19.1.25
Date:
01-Aug-99     Release date:   10-Jan-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q00403  (TF2B_HUMAN) -  Transcription initiation factor IIB
Seq:
Struc: 		316 a.a.
207 a.a.
Protein chains
Pfam   ArchSchema ?
P20226  (TBP_HUMAN) -  TATA-box-binding protein
Seq:
Struc: 		339 a.a.
180 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     regulation of transcription, DNA-dependent   4 terms 
  Biochemical function     transcription regulator activity     7 terms  

 

 
DOI no: 10.1093/emboj/19.1.25 EMBO J 19:25-36 (2000)
PubMed id: 10619841  
 
 
Structural basis of preinitiation complex assembly on human pol II promoters.
F.T.Tsai, P.B.Sigler.
 
  ABSTRACT  
 
Transcription initiation requires the assembly of a preinitiation complex (PIC), which is nucleated through binding of the TATA-box binding protein (TBP) to the promoter. Biochemical studies have shown, however, that TBP recognizes the TATA-box in both orientations and, therefore, cannot account for the directionality of PIC assembly. Transcription factor IIB (TFIIB) is essential for transcription initiation from RNA polymerase II promoters. Recent functional studies have identified a specific 7 bp TFIIB recognition element (BRE) immediately upstream of the TATA-box. We present here the 2.65 A resolution crystal structure of a human TFIIBc-TBPc complex bound to an idealized and extended adenovirus major late promoter. This structure now reveals that human TFIIBc binds to the promoter asymmetrically through base-specific contacts in the major groove upstream and in the minor groove downstream of the TATA-box. Binding of TFIIBc is, therefore, synergistic with TBPc requiring the distortion of the TATA-box. Thus, the newly described TFIIBc-DNA interface is likely to be a key determinant for the unidirectional assembly of a functional PIC.
 
  Selected figure(s)  
 
Figure 5.
Figure 5 (A) Stereo view depicting the molecular interactions between the 'recognition-helix' BH5' (green) of the HTH and the BRE. Amino acid residues (green) that contact the major groove are labeled accordingly. For clarity, only the bases of the coding strand (yellow) are labeled. Water molecules are shown as orange spheres. A black line indicates hydrogen bonds. (B and C) HTH motif consisting of helices BH4' and BH5' of hTFIIBc. The view in (C) is similar to (B) rotated by 90° around the DNA helical axis. Label and color designations are as described in (A) and Figures 1 and 2A. Figures were generated with MOLSCRIPT/RASTER3D (Kraulis, 1991; Merritt and Bacon, 1997). 		Figure 6.
Figure 6 (A) Stereo view depicting the molecular interactions between the minor groove recognition-loop (residues 152–156 of hTFIIBc) and the MLP immediately downstream of the TATA-box. The color designation is the same as in Figures 1 and 2A. For clarity, only the bases of the coding strand (yellow) are labeled. The figure was generated with MOLSCRIPT/RASTER3D (Kraulis, 1991; Merritt and Bacon, 1997). (B) Alignment of the minor groove recognition-loop sequences of eukaryal and archaeal TF(II)Bs. Green highlighting indicates conserved, and yellow highly similar residues. An asterisk indicates a residue in hTFIIBc that contacts the minor groove in the current structure.
 
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2000, 19, 25-36) copyright 2000.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21071415 M.Q.Yang, K.Laflamme, V.Gotea, C.H.Joiner, N.E.Seidel, C.Wong, H.M.Petrykowska, J.Lichtenberg, S.Lee, L.Welch, P.G.Gallagher, D.M.Bodine, and L.Elnitski (2011).
Genome-wide detection of a TFIID localization element from an initial human disease mutation.
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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.  
21502537 S.Liu, M.Balasov, H.Wang, L.Wu, I.N.Chesnokov, and Y.Liu (2011).
Structural analysis of human Orc6 protein reveals a homology with transcription factor TFIIB.
  Proc Natl Acad Sci U S A, 108, 7373-7378.
PDB code: 3m03
20230619 T.K.Albert, K.Grote, S.Boeing, and M.Meisterernst (2010).
Basal core promoters control the equilibrium between negative cofactor 2 and preinitiation complexes in human cells.
  Genome Biol, 11, R33.  
20222994 V.Bernard, V.Brunaud, and A.Lecharny (2010).
TC-motifs at the TATA-box expected position in plant genes: a novel class of motifs involved in the transcription regulation.
  BMC Genomics, 11, 166.  
21164480 W.W.Tsai, Z.Wang, T.T.Yiu, K.C.Akdemir, W.Xia, S.Winter, C.Y.Tsai, X.Shi, D.Schwarzer, W.Plunkett, B.Aronow, O.Gozani, W.Fischle, M.C.Hung, D.J.Patel, and M.C.Barton (2010).
TRIM24 links a non-canonical histone signature to breast cancer.
  Nature, 468, 927-932.
PDB codes: 3o33 3o34 3o35 3o36 3o37
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
19393049 A.Marathe, D.Karandur, and M.Bansal (2009).
Small local variations in B-form DNA lead to a large variety of global geometries which can accommodate most DNA-binding protein motifs.
  BMC Struct Biol, 9, 24.  
19666603 B.S.Ibrahim, N.Kanneganti, G.E.Rieckhof, A.Das, D.V.Laurents, J.B.Palenchar, V.Bellofatto, and D.A.Wah (2009).
Structure of the C-terminal domain of transcription factor IIB from Trypanosoma brucei.
  Proc Natl Acad Sci U S A, 106, 13242-13247.
PDB code: 3h4c
19750005 H.G.Chen, W.J.Han, M.Deng, J.Qin, D.Yuan, J.P.Liu, L.Xiao, L.Gong, S.Liang, J.Zhang, Y.Liu, and D.W.Li (2009).
Transcriptional regulation of PP2A-A alpha is mediated by multiple factors including AP-2alpha, CREB, ETS-1, and SP-1.
  PLoS One, 4, e7019.  
19359364 J.Zhang, E.Li, and G.J.Olsen (2009).
Protein-coding gene promoters in Methanocaldococcus (Methanococcus) jannaschii.
  Nucleic Acids Res, 37, 3588-3601.  
19515240 M.E.Pitulescu, M.Teichmann, L.Luo, and M.Kessel (2009).
TIPT2 and geminin interact with basal transcription factors to synergize in transcriptional regulation.
  BMC Biochem, 10, 16.  
19007415 M.Ouhammouch, W.Hausner, and E.P.Geiduschek (2009).
TBP domain symmetry in basal and activated archaeal transcription.
  Mol Microbiol, 71, 123-131.  
18704949 S.Biswas, M.Guharoy, and P.Chakrabarti (2009).
Dissection, residue conservation, and structural classification of protein-DNA interfaces.
  Proteins, 74, 643-654.  
19114554 W.Deng, B.Malecová, T.Oelgeschläger, and S.G.Roberts (2009).
TFIIB recognition elements control the TFIIA-NC2 axis in transcriptional regulation.
  Mol Cell Biol, 29, 1389-1400.  
18981048 E.Li, C.I.Reich, and G.J.Olsen (2008).
A whole-genome approach to identifying protein binding sites: promoters in Methanocaldococcus (Methanococcus) jannaschii.
  Nucleic Acids Res, 36, 6948-6958.  
17214883 F.Spyrakis, P.Cozzini, C.Bertoli, A.Marabotti, G.E.Kellogg, and A.Mozzarelli (2007).
Energetics of the protein-DNA-water interaction.
  BMC Struct Biol, 7, 4.  
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.  
17283052 M.Balasov, R.P.Huijbregts, and I.Chesnokov (2007).
Role of the Orc6 protein in origin recognition complex-dependent DNA binding and replication in Drosophila melanogaster.
  Mol Cell Biol, 27, 3143-3153.  
17593382 W.Deng, and S.G.Roberts (2007).
TFIIB and the regulation of transcription by RNA polymerase II.
  Chromosoma, 116, 417-429.  
16554554 B.Schimanski, J.Brandenburg, T.N.Nguyen, M.J.Caimano, and A.Günzl (2006).
A TFIIB-like protein is indispensable for spliced leader RNA gene transcription in Trypanosoma brucei.
  Nucleic Acids Res, 34, 1676-1684.  
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.  
16790048 N.I.Gershenzon, E.N.Trifonov, and I.P.Ioshikhes (2006).
The features of Drosophila core promoters revealed by statistical analysis.
  BMC Genomics, 7, 161.  
16531235 P.Grob, M.J.Cruse, C.Inouye, M.Peris, P.A.Penczek, R.Tjian, and E.Nogales (2006).
Cryo-electron microscopy studies of human TFIID: conformational breathing in the integration of gene regulatory cues.
  Structure, 14, 511-520.  
16885025 Y.Takagi, G.Calero, H.Komori, J.A.Brown, A.H.Ehrensberger, A.Hudmon, F.Asturias, and R.D.Kornberg (2006).
Head module control of mediator interactions.
  Mol Cell, 23, 355-364.  
15733318 C.Molina, and E.Grotewold (2005).
Genome wide analysis of Arabidopsis core promoters.
  BMC Genomics, 6, 25.  
15916593 E.P.Geiduschek, and M.Ouhammouch (2005).
Archaeal transcription and its regulators.
  Mol Microbiol, 56, 1397-1407.  
16227432 G.A.Kassavetis, E.Soragni, R.Driscoll, and E.P.Geiduschek (2005).
Reconfiguring the connectivity of a multiprotein complex: fusions of yeast TATA-binding protein with Brf1, and the function of transcription factor IIIB.
  Proc Natl Acad Sci U S A, 102, 15406-15411.  
15572469 N.I.Gershenzon, and I.P.Ioshikhes (2005).
Synergy of human Pol II core promoter elements revealed by statistical sequence analysis.
  Bioinformatics, 21, 1295-1300.  
15951513 P.Somboonthum, H.Ohta, S.Yamada, M.Onishi, A.Ike, Y.Nishimune, and M.Nozaki (2005).
cAMP-responsive element in TATA-less core promoter is essential for haploid-specific gene expression in mouse testis.
  Nucleic Acids Res, 33, 3401-3411.  
16230532 W.Deng, and S.G.Roberts (2005).
A core promoter element downstream of the TATA box that is recognized by TFIIB.
  Genes Dev, 19, 2418-2423.  
14963322 D.A.Bushnell, K.D.Westover, R.E.Davis, and R.D.Kornberg (2004).
Structural basis of transcription: an RNA polymerase II-TFIIB cocrystal at 4.5 Angstroms.
  Science, 303, 983-988.
PDB code: 1r5u
15093825 F.J.Asturias (2004).
RNA polymerase II structure, and organization of the preinitiation complex.
  Curr Opin Struct Biol, 14, 121-129.  
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.  
14597623 M.B.Renfrow, N.Naryshkin, L.M.Lewis, H.T.Chen, R.H.Ebright, and R.A.Scott (2004).
Transcription factor B contacts promoter DNA near the transcription start site of the archaeal transcription initiation complex.
  J Biol Chem, 279, 2825-2831.  
14617625 M.S.Bartlett, M.Thomm, and E.P.Geiduschek (2004).
Topography of the euryarchaeal transcription initiation complex.
  J Biol Chem, 279, 5894-5903.  
15044803 P.Aloy, B.Böttcher, H.Ceulemans, C.Leutwein, C.Mellwig, S.Fischer, A.C.Gavin, P.Bork, G.Superti-Furga, L.Serrano, and R.B.Russell (2004).
Structure-based assembly of protein complexes in yeast.
  Science, 303, 2026-2029.  
15024075 T.C.Tubon, W.P.Tansey, and W.Herr (2004).
A nonconserved surface of the TFIIB zinc ribbon domain plays a direct role in RNA polymerase II recruitment.
  Mol Cell Biol, 24, 2863-2874.  
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.  
12878722 I.N.Chesnokov, O.N.Chesnokova, and M.Botchan (2003).
A cytokinetic function of Drosophila ORC6 protein resides in a domain distinct from its replication activity.
  Proc Natl Acad Sci U S A, 100, 9150-9155.  
  12672487 J.C.Reese (2003).
Basal transcription factors.
  Curr Opin Genet Dev, 13, 114-118.  
14517249 O.Schröder, G.O.Bryant, E.P.Geiduschek, A.J.Berk, and G.A.Kassavetis (2003).
A common site on TBP for transcription by RNA polymerases II and III.
  EMBO J, 22, 5115-5124.  
12969427 P.Achard, T.Lagrange, A.F.El-Zanaty, and R.Mache (2003).
Architecture and transcriptional activity of the initiator element of the TATA-less RPL21 gene.
  Plant J, 35, 743-752.  
12651739 S.T.Smale, and J.T.Kadonaga (2003).
The RNA polymerase II core promoter.
  Annu Rev Biochem, 72, 449-479.  
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.  
14585974 X.Zhao, and W.Herr (2003).
Role of the inhibitory DNA-binding surface of human TATA-binding protein in recruitment of human TFIIB family members.
  Mol Cell Biol, 23, 8152-8160.  
12743036 Z.A.Felton-Edkins, J.A.Fairley, E.L.Graham, I.M.Johnston, R.J.White, and P.H.Scott (2003).
The mitogen-activated protein (MAP) kinase ERK induces tRNA synthesis by phosphorylating TFIIIB.
  EMBO J, 22, 2422-2432.  
14517303 Z.Chen, and J.L.Manley (2003).
Core promoter elements and TAFs contribute to the diversity of transcriptional activation in vertebrates.
  Mol Cell Biol, 23, 7350-7362.  
11863454 A.R.Kays, and A.Schepartz (2002).
Gal4-VP16 and Gal4-AH increase the orientational and axial specificity of TATA box recognition by TATA box binding protein.
  Biochemistry, 41, 3147-3155.  
11865052 J.A.Ehley, C.Melander, D.Herman, E.E.Baird, H.A.Ferguson, J.A.Goodrich, P.B.Dervan, and J.M.Gottesfeld (2002).
Promoter scanning for transcription inhibition with DNA-binding polyamides.
  Mol Cell Biol, 22, 1723-1733.  
12215527 J.A.Fairley, R.Evans, N.A.Hawkes, and S.G.Roberts (2002).
Core promoter-dependent TFIIB conformation and a role for TFIIB conformation in transcription start site selection.
  Mol Cell Biol, 22, 6697-6705.  
12446791 J.V.Spencer, and K.M.Arndt (2002).
A TATA binding protein mutant with increased affinity for DNA directs transcription from a reversed TATA sequence in vivo.
  Mol Cell Biol, 22, 8744-8755.  
12016223 P.Cabart, and S.Murphy (2002).
Assembly of human small nuclear RNA gene-specific transcription factor IIIB complex de novo on and off promoter.
  J Biol Chem, 277, 26831-26838.  
11606563 C.P.Magill, S.P.Jackson, and S.D.Bell (2001).
Identification of a conserved archaeal RNA polymerase subunit contacted by the basal transcription factor TFB.
  J Biol Chem, 276, 46693-46696.  
11179888 C.W.Müller (2001).
Transcription factors: global and detailed views.
  Curr Opin Struct Biol, 11, 26-32.  
11461703 K.Kamada, F.Shu, H.Chen, S.Malik, G.Stelzer, R.G.Roeder, M.Meisterernst, and S.K.Burley (2001).
Crystal structure of negative cofactor 2 recognizing the TBP-DNA transcription complex.
  Cell, 106, 71-81.
PDB code: 1jfi
11564744 P.Cabart, and S.Murphy (2001).
BRFU, a TFIIB-like factor, is directly recruited to the TATA-box of polymerase III small nuclear RNA gene promoters through its interaction with TATA-binding protein.
  J Biol Chem, 276, 43056-43064.  
11711430 R.Evans, J.A.Fairley, and S.G.Roberts (2001).
Activator-mediated disruption of sequence-specific DNA contacts by the general transcription factor TFIIB.
  Genes Dev, 15, 2945-2949.  
11223526 S.M.Wang, G.J.Kim, and D.T.Gewirth (2001).
Structural studies of a yeast quaternary transcription-initiation complex.
  Acta Crystallogr D Biol Crystallogr, 57, 441-444.  
  11048951 A.R.Kays, and A.Schepartz (2000).
Virtually unidirectional binding of TBP to the AdMLP TATA box within the quaternary complex with TFIIA and TFIIB.
  Chem Biol, 7, 601-610.  
11046131 D.L.Pappas, and M.Hampsey (2000).
Functional interaction between Ssu72 and the Rpb2 subunit of RNA polymerase II in Saccharomyces cerevisiae.
  Mol Cell Biol, 20, 8343-8351.  
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.