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PDBsum entry 1cdw

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protein dna_rna links
Transcription/DNA PDB id
1cdw
Jmol
Contents
Protein chain
179 a.a. *
DNA/RNA
Waters ×280
* Residue conservation analysis
PDB id:
1cdw
Name: Transcription/DNA
Title: Human tbp core domain complexed with DNA
Structure: DNA (5'- d( Cp Tp Gp Cp Tp Ap Tp Ap Ap Ap Ap Gp Gp Cp Tp G)-3'). Chain: b. Engineered: yes. DNA (5'- d( Cp Ap Gp Cp Cp Tp Tp Tp Tp Ap Tp Ap Gp Cp Ap G)-3'). Chain: c. Engineered: yes. Protein (tata binding protein (tbp)).
Source: Synthetic: yes. Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
1.90Å     R-factor:   0.189     R-free:   0.258
Authors: D.B.Nikolov,H.Chen,E.D.Halay,A.Hoffmann,R.G.Roeder, S.K.Burley
Key ref: D.B.Nikolov et al. (1996). Crystal structure of a human TATA box-binding protein/TATA element complex. Proc Natl Acad Sci U S A, 93, 4862-4867. PubMed id: 8643494
Date:
11-Apr-96     Release date:   23-Dec-96    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P20226  (TBP_HUMAN) -  TATA-box-binding protein
Seq:
Struc:
339 a.a.
179 a.a.*
Key:    PfamA 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     transcription initiation, DNA-dependent   1 term 
  Biochemical function     DNA binding     1 term  

 

 
Proc Natl Acad Sci U S A 93:4862-4867 (1996)
PubMed id: 8643494  
 
 
Crystal structure of a human TATA box-binding protein/TATA element complex.
D.B.Nikolov, H.Chen, E.D.Halay, A.Hoffman, R.G.Roeder, S.K.Burley.
 
  ABSTRACT  
 
The TATA box-binding protein (TBP) is required by all three eukaryotic RNA polymerases for correct initiation of transcription of ribosomal, messenger, small nuclear, and transfer RNAs. The cocrystal structure of the C-terminal/core region of human TBP complexed with the TATA element of the adenovirus major late promoter has been determined at 1.9 angstroms resolution. Structural and functional analyses of the protein-DNA complex are presented, with a detailed comparison to our 1.9-angstroms resolution structure of Arabidopsis thaliana TBP2 bound to the same TATA box.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
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Archaeal RNA polymerase and transcription regulation.
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Xanthomonas AvrBs3 family-type III effectors: discovery and function.
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20687914 S.A.Gokhale, R.Roshan, V.Khetan, B.Pillai, and C.J.Gadgil (2010).
A kinetic model of TBP auto-regulation exhibits bistability.
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19090532 M.Varedian, M.Erdélyi, A.Persson, and A.Gogoll (2009).
Interplaying factors for the formation of photoswitchable beta-hairpins: the advantage of a flexible switch.
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19304790 S.Takiya, S.Saito, T.Yokoyama, D.Matsumoto, T.Aizawa, M.Kamiya, M.Demura, and K.Kawano (2009).
DNA-binding property of the novel DNA-binding domain STPR in FMBP-1 of the silkworm Bombyx mori.
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19228197 T.Tadokoro, and S.Kanaya (2009).
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18385157 G.Bjornsdottir, and L.C.Myers (2008).
Minimal components of the RNA polymerase II transcription apparatus determine the consensus TATA box.
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18326635 J.H.Bredenberg, C.Russo, and M.O.Fenley (2008).
Salt-mediated electrostatics in the association of TATA binding proteins to DNA: a combined molecular mechanics/Poisson-Boltzmann study.
  Biophys J, 94, 4634-4645.  
17576671 H.Faiger, M.Ivanchenko, and T.E.Haran (2007).
Nearest-neighbor non-additivity versus long-range non-additivity in TATA-box structure and its implications for TBP-binding mechanism.
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18159946 M.Brenneis, O.Hering, C.Lange, and J.Soppa (2007).
Experimental characterization of Cis-acting elements important for translation and transcription in halophilic archaea.
  PLoS Genet, 3, e229.  
17517143 R.A.Hitchcock, S.Thomas, D.A.Campbell, and N.R.Sturm (2007).
The promoter and transcribed regions of the Leishmania tarentolae spliced leader RNA gene array are devoid of nucleosomes.
  BMC Microbiol, 7, 44.  
17378582 S.Khrapunov, and M.Brenowitz (2007).
Influence of the N-terminal domain and divalent cations on self-association and DNA binding by the Saccharomyces cerevisiae TATA binding protein.
  Biochemistry, 46, 4876-4887.  
17403692 S.Teodorovic, C.D.Walls, and H.G.Elmendorf (2007).
Bidirectional transcription is an inherent feature of Giardia lamblia promoters and contributes to an abundance of sterile antisense transcripts throughout the genome.
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17923679 T.Chung, O.Siol, T.Dingermann, and T.Winckler (2007).
Protein interactions involved in tRNA gene-specific integration of Dictyostelium discoideum non-long terminal repeat retrotransposon TRE5-A.
  Mol Cell Biol, 27, 8492-8501.  
17401341 Y.Xu, R.Tashiro, and H.Sugiyama (2007).
Photochemical determination of different DNA structures.
  Nat Protoc, 2, 78-87.  
16407329 H.Faiger, M.Ivanchenko, I.Cohen, and T.E.Haran (2006).
TBP flanking sequences: asymmetry of binding, long-range effects and consensus sequences.
  Nucleic Acids Res, 34, 104-119.  
16965535 I.Wierstra, and J.Alves (2006).
FOXM1c transactivates the human c-myc promoter directly via the two TATA boxes P1 and P2.
  FEBS J, 273, 4645-4667.  
16698780 M.Zacharias (2006).
Minor groove deformability of DNA: a molecular dynamics free energy simulation study.
  Biophys J, 91, 882-891.  
16387764 Q.Zhang, and T.Schlick (2006).
Stereochemistry and position-dependent effects of carcinogens on TATA/TBP binding.
  Biophys J, 90, 1865-1877.  
16481311 S.L.Williams, L.K.Parkhurst, and L.J.Parkhurst (2006).
Changes in DNA bending and flexing due to tethered cations detected by fluorescence resonance energy transfer.
  Nucleic Acids Res, 34, 1028-1035.  
16416452 Y.Xu, and H.Sugiyama (2006).
Photochemical approach to probing different DNA structures.
  Angew Chem Int Ed Engl, 45, 1354-1362.  
16387868 Z.Wang, G.M.Jones, and G.Prelich (2006).
Genetic analysis connects SLX5 and SLX8 to the SUMO pathway in Saccharomyces cerevisiae.
  Genetics, 172, 1499-1509.  
16103159 A.François, M.Guilbaud, R.Awedikian, G.Chadeuf, P.Moullier, and A.Salvetti (2005).
The cellular TATA binding protein is required for rep-dependent replication of a minimal adeno-associated virus type 2 p5 element.
  J Virol, 79, 11082-11094.  
15939933 A.Kanhere, and M.Bansal (2005).
Structural properties of promoters: similarities and differences between prokaryotes and eukaryotes.
  Nucleic Acids Res, 33, 3165-3175.  
15653643 C.Y.Chen, T.P.Ko, T.W.Lin, C.C.Chou, C.J.Chen, and A.H.Wang (2005).
Probing the DNA kink structure induced by the hyperthermophilic chromosomal protein Sac7d.
  Nucleic Acids Res, 33, 430-438.
PDB codes: 1wto 1wtp 1wtq 1wtr 1wtv 1wtw 1wtx 1xyi
15752353 G.de Dios-Bravo, J.P.Luna-Arias, A.M.Riverón, J.J.Olivares-Trejo, C.López-Camarillo, and E.Orozco (2005).
Entamoeba histolytica TATA-box binding protein binds to different TATA variants in vitro.
  FEBS J, 272, 1354-1366.  
16179647 M.P.Klejman, X.Zhao, F.M.van Schaik, W.Herr, and H.T.Timmers (2005).
Mutational analysis of BTAF1-TBP interaction: BTAF1 can rescue DNA-binding defective TBP mutants.
  Nucleic Acids Res, 33, 5426-5436.  
15746285 R.A.O'Flanagan, G.Paillard, R.Lavery, and A.M.Sengupta (2005).
Non-additivity in protein-DNA binding.
  Bioinformatics, 21, 2254-2263.  
15468320 A.Gutmanas, and M.Billeter (2004).
Specific DNA recognition by the Antp homeodomain: MD simulations of specific and nonspecific complexes.
  Proteins, 57, 772-782.  
15139817 B.Jayaram, and T.Jain (2004).
The role of water in protein-DNA recognition.
  Annu Rev Biophys Biomol Struct, 33, 343-361.  
14725771 G.Paillard, and R.Lavery (2004).
Analyzing protein-DNA recognition mechanisms.
  Structure, 12, 113-122.  
15614969 N.Adachi, R.Natsume, M.Senda, S.Muto, T.Senda, and M.Horikoshi (2004).
Purification, crystallization and preliminary X-ray analysis of Methanococcus jannaschii TATA box-binding protein (TBP).
  Acta Crystallogr D Biol Crystallogr, 60, 2328-2331.  
15226442 P.Eriksson, D.Biswas, Y.Yu, J.M.Stewart, and D.J.Stillman (2004).
TATA-binding protein mutants that are lethal in the absence of the Nhp6 high-mobility-group protein.
  Mol Cell Biol, 24, 6419-6429.  
12799489 A.K.Mishra, P.Vanathi, and P.Bhargava (2003).
The transcriptional activator GAL4-VP16 regulates the intra-molecular interactions of the TATA-binding protein.
  J Biosci, 28, 423-436.  
12767124 D.Strahs, D.Barash, X.Qian, and T.Schlick (2003).
Sequence-dependent solution structure and motions of 13 TATA/TBP (TATA-box binding protein) complexes.
  Biopolymers, 69, 216-243.  
12711677 P.Rai, T.D.Cole, E.Thompson, D.P.Millar, and S.Linn (2003).
Steady-state and time-resolved fluorescence studies indicate an unusual conformation of 2-aminopurine within ATAT and TATA duplex DNA sequences.
  Nucleic Acids Res, 31, 2323-2332.  
12799488 P.Vanathi, A.K.Mishra, and P.Bhargava (2003).
Regulation of activity of the yeast TATA-binding protein through intra-molecular interactions.
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12651739 S.T.Smale, and J.T.Kadonaga (2003).
The RNA polymerase II core promoter.
  Annu Rev Biochem, 72, 449-479.  
12609498 S.Wells, and D.Murphy (2003).
Transgenic studies on the regulation of the anterior pituitary gland function by the hypothalamus.
  Front Neuroendocrinol, 24, 11-26.  
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.  
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.  
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.  
11909971 L.S.Martel, H.J.Brown, and A.J.Berk (2002).
Evidence that TAF-TATA box-binding protein interactions are required for activated transcription in mammalian cells.
  Mol Cell Biol, 22, 2788-2798.  
12191469 M.P.Cosma (2002).
Ordered recruitment: gene-specific mechanism of transcription activation.
  Mol Cell, 10, 227-236.  
11438706 J.Hizver, H.Rozenberg, F.Frolow, D.Rabinovich, and Z.Shakked (2001).
DNA bending by an adenine--thymine tract and its role in gene regulation.
  Proc Natl Acad Sci U S A, 98, 8490-8495.
PDB code: 1ilc
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
11987180 L.J.Parkhurst, K.M.Parkhurst, R.Powell, J.Wu, and S.Williams (2001).
Time-resolved fluorescence resonance energy transfer studies of DNA bending in double-stranded oligonucleotides and in DNA-protein complexes.
  Biopolymers, 61, 180-200.  
11327862 S.Bergqvist, R.O'Brien, and J.E.Ladbury (2001).
Site-specific cation binding mediates TATA binding protein-DNA interaction from a hyperthermophilic archaeon.
  Biochemistry, 40, 2419-2425.  
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.  
10619841 F.T.Tsai, and P.B.Sigler (2000).
Structural basis of preinitiation complex assembly on human pol II promoters.
  EMBO J, 19, 25-36.
PDB code: 1c9b
11754342 I.Lafontaine, and R.Lavery (2000).
ADAPT: a molecular mechanics approach for studying the structural properties of long DNA sequences.
  Biopolymers, 56, 292-310.  
10736150 J.D.Kahn (2000).
Topological effects of the TATA box binding protein on minicircle DNA and a possible thermodynamic linkage to chromatin remodeling.
  Biochemistry, 39, 3520-3524.  
11092925 N.Potier, V.Lamour, A.Poterszman, J.C.Thierry, D.Moras, and A.Van Dorsselaer (2000).
Characterization of crystal content by ESI-MS and MALDI-MS.
  Acta Crystallogr D Biol Crystallogr, 56, 1583-1590.  
10594036 Y.G.Gangloff, S.Werten, C.Romier, L.Carré, O.Poch, D.Moras, and I.Davidson (2000).
The human TFIID components TAF(II)135 and TAF(II)20 and the yeast SAGA components ADA1 and TAF(II)68 heterodimerize to form histone-like pairs.
  Mol Cell Biol, 20, 340-351.  
10647173 J.Janin (1999).
Wet and dry interfaces: the role of solvent in protein-protein and protein-DNA recognition.
  Structure, 7, R277-R279.  
  10373570 J.Persinger, S.M.Sengupta, and B.Bartholomew (1999).
Spatial organization of the core region of yeast TFIIIB-DNA complexes.
  Mol Cell Biol, 19, 5218-5234.  
10385521 L.F.Pemberton, J.S.Rosenblum, and G.Blobel (1999).
Nuclear import of the TATA-binding protein: mediation by the karyopherin Kap114p and a possible mechanism for intranuclear targeting.
  J Cell Biol, 145, 1407-1417.  
10570130 O.Littlefield, Y.Korkhin, and P.B.Sigler (1999).
The structural basis for the oriented assembly of a TBP/TFB/promoter complex.
  Proc Natl Acad Sci U S A, 96, 13668-13673.
PDB code: 1d3u
10570129 S.D.Bell, P.L.Kosa, P.B.Sigler, and S.P.Jackson (1999).
Orientation of the transcription preinitiation complex in archaea.
  Proc Natl Acad Sci U S A, 96, 13662-13667.  
9646864 C.A.Bewley, A.M.Gronenborn, and G.M.Clore (1998).
Minor groove-binding architectural proteins: structure, function, and DNA recognition.
  Annu Rev Biophys Biomol Struct, 27, 105-131.  
9746540 C.Bamdad (1998).
The use of variable density self-assembled monolayers to probe the structure of a target molecule.
  Biophys J, 75, 1989-1996.  
9670810 D.Dittmer, and D.H.Kedes (1998).
Do viral chemokines modulate Kaposi's sarcoma?
  Bioessays, 20, 367-370.  
10384273 D.Reinberg, G.Orphanides, R.Ebright, S.Akoulitchev, J.Carcamo, H.Cho, P.Cortes, R.Drapkin, O.Flores, I.Ha, J.A.Inostroza, S.Kim, T.K.Kim, P.Kumar, T.Lagrange, G.LeRoy, H.Lu, D.M.Ma, E.Maldonado, A.Merino, F.Mermelstein, I.Olave, M.Sheldon, R.Shiekhattar, and L.Zawel (1998).
The RNA polymerase II general transcription factors: past, present, and future.
  Cold Spring Harb Symp Quant Biol, 63, 83.  
9667920 J.M.Cox, A.R.Kays, J.F.Sanchez, and A.Schepartz (1998).
Preinitation complex assembly: potentially a bumpy path.
  Curr Opin Chem Biol, 2, 11-17.  
9591646 L.Pardo, N.Pastor, and H.Weinstein (1998).
Progressive DNA bending is made possible by gradual changes in the torsion angle of the glycosyl bond.
  Biophys J, 74, 2191-2198.  
9788936 L.Pardo, N.Pastor, and H.Weinstein (1998).
Selective binding of the TATA box-binding protein to the TATA box-containing promoter: analysis of structural and energetic factors.
  Biophys J, 75, 2411-2421.  
9518483 R.E.Dickerson (1998).
DNA bending: the prevalence of kinkiness and the virtues of normality.
  Nucleic Acids Res, 26, 1906-1926.  
9501975 R.Hori, and M.Carey (1998).
Transcription: TRF walks the walk but can it talk the talk?
  Curr Biol, 8, R124-R127.  
10384268 S.K.Burley (1998).
X-ray crystallographic studies of eukaryotic transcription factors.
  Cold Spring Harb Symp Quant Biol, 63, 33-40.  
9519295 S.Tan, and T.J.Richmond (1998).
Eukaryotic transcription factors.
  Curr Opin Struct Biol, 8, 41-48.  
  9733880 T.R.Serio, N.Cahill, M.E.Prout, and G.Miller (1998).
A functionally distinct TATA box required for late progression through the Epstein-Barr virus life cycle.
  J Virol, 72, 8338-8343.  
9843390 V.Petri, M.Hsieh, E.Jamison, and M.Brenowitz (1998).
DNA sequence-specific recognition by the Saccharomyces cerevisiae "TATA" binding protein: promoter-dependent differences in the thermodynamics and kinetics of binding.
  Biochemistry, 37, 15842-15849.  
9016721 D.Grate, and C.Wilson (1997).
Role REVersal: understanding how RRE RNA binds its peptide ligand.
  Structure, 5, 7.  
9241421 G.Patikoglou, and S.K.Burley (1997).
Eukaryotic transcription factor-DNA complexes.
  Annu Rev Biophys Biomol Struct, 26, 289-325.  
  8985328 H.Lu, M.D.Reach, E.Minaya, and C.S.Young (1997).
The initiator element of the adenovirus major late promoter has an important role in transcription initiation in vivo.
  J Virol, 71, 102-109.  
9391050 J.M.Cox, M.M.Hayward, J.F.Sanchez, L.D.Gegnas, S.van der Zee, J.H.Dennis, P.B.Sigler, and A.Schepartz (1997).
Bidirectional binding of the TATA box binding protein to the TATA box.
  Proc Natl Acad Sci U S A, 94, 13475-13480.  
9032063 J.W.Schwabe (1997).
The role of water in protein-DNA interactions.
  Curr Opin Struct Biol, 7, 126-134.  
9782775 M.Tateno, K.Yamasaki, N.Amano, J.Kakinuma, H.Koike, M.D.Allen, and M.Suzuki (1997).
DNA recognition by beta-sheets.
  Biopolymers, 44, 335-359.  
9251783 N.Pastor, L.Pardo, and H.Weinstein (1997).
Does TATA matter? A structural exploration of the selectivity determinants in its complexes with TATA box-binding protein.
  Biophys J, 73, 640-652.  
9177165 P.F.Kosa, G.Ghosh, B.S.DeDecker, and P.B.Sigler (1997).
The 2.1-A crystal structure of an archaeal preinitiation complex: TATA-box-binding protein/transcription factor (II)B core/TATA-box.
  Proc Natl Acad Sci U S A, 94, 6042-6047.
PDB code: 1ais
9241250 P.Hardenbol, J.C.Wang, and M.W.Van Dyke (1997).
Identification of preferred hTBP DNA binding sites by the combinatorial method REPSA.
  Nucleic Acids Res, 25, 3339-3344.  
9207072 R.A.Coleman, and B.F.Pugh (1997).
Slow dimer dissociation of the TATA binding protein dictates the kinetics of DNA binding.
  Proc Natl Acad Sci U S A, 94, 7221-7226.  
9782776 R.E.Dickerson, and T.K.Chiu (1997).
Helix bending as a factor in protein/DNA recognition.
  Biopolymers, 44, 361-403.  
  9111361 W.S.Blair, and B.R.Cullen (1997).
A yeast TATA-binding protein mutant that selectively enhances gene expression from weak RNA polymerase II promoters.
  Mol Cell Biol, 17, 2888-2896.  
8855228 T.Lagrange, T.K.Kim, G.Orphanides, Y.W.Ebright, R.H.Ebright, and D.Reinberg (1996).
High-resolution mapping of nucleoprotein complexes by site-specific protein-DNA photocrosslinking: organization of the human TBP-TFIIA-TFIIB-DNA quaternary complex.
  Proc Natl Acad Sci U S A, 93, 10620-10625.  
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.