Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
302  structures 1856  species 0  interactions 7937  sequences 60  architectures

Family: TBP (PF00352)

Summary: Transcription factor TFIID (or TATA-binding protein, TBP)

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "TATA-binding protein". More...

TATA-binding protein Edit Wikipedia article

Protein TBP PDB 1c9b.png
Available structures
PDBOrtholog search: PDBe RCSB
AliasesTBP, GTF2D, GTF2D1, HDL4, SCA17, TFIID, TATA-box binding protein, TATA-binding protein, TBP1
External IDsOMIM: 600075 MGI: 101838 HomoloGene: 2404 GeneCards: TBP
RefSeq (mRNA)



RefSeq (protein)



Location (UCSC)Chr 6: 170.55 – 170.57 Mbn/a
PubMed search[2][3]
View/Edit HumanView/Edit Mouse
PDB 1ngm EBI.jpg
crystal structure of a yeast brf1-tbp-dna ternary complex
Pfam clanCL0407

The TATA-binding protein (TBP) is a general transcription factor that binds specifically to a DNA sequence called the TATA box. This DNA sequence is found about 30 base pairs upstream of the transcription start site in some eukaryotic gene promoters.[4]

TBP gene family

TBP is a member of a small gene family of TBP-related factors.[5] The first TBP-related factor (TRF/TRF1) was identified in the fruit fly Drosophila, but appears to be fly or insect-specific. Subsequently TBPL1/TRF2 was found in the genomes of many metazoans, whereas vertebrate genomes encode a third vertebrate family member, TBPL2/TRF3. In specific cell types or on specific promoters TBP can be replaced by one of these TBP-related factors, some of which interact with the TATA box similarly to TBP.

Role as transcription factor

TBP is a subunit of the eukaryotic general transcription factor TFIID. TFIID is the first protein to bind to DNA during the formation of the transcription preinitiation complex of RNA polymerase II (RNA Pol II).[6] As one of the few proteins in the preinitiation complex that binds DNA in a sequence-specific manner, it helps position RNA polymerase II over the transcription start site of the gene. However, it is estimated that only 10–20% of human promoters have TATA boxes. Therefore, TBP is probably not the only protein involved in positioning RNA polymerase II. Majority of human promoters are TATA-less housekeeping gene promoters. The binding of TBP to these promoters is facilitated by housekeeping gene regulators.[7][8] Interestingly, transcription initiates within a narrow region at around 30 bp downstream of TATA box on TATA-containing promoters,[9] while transcription start sites of TATA-less promoters are dispersed within a 200 bp region.[10][8]

Binding of TFIID to the TATA box in the promoter region of the gene initiates the recruitment of other factors required for RNA Pol II to begin transcription. Some of the other recruited transcription factors include TFIIA, TFIIB, and TFIIF. Each of these transcription factors contains several protein subunits.

TBP is also important for transcription by RNA polymerase I and RNA polymerase III, and is therefore involved in transcription initiation by all three RNA polymerases.[11]

TBP is involved in DNA melting (double strand separation) by bending the DNA by 80° (the AT-rich sequence to which it binds facilitates easy melting). The TBP is an unusual protein in that it binds the minor groove using a β sheet.

Another distinctive feature of TBP is a long string of glutamines in the N-terminus of the protein. This region modulates the DNA binding activity of the C-terminus, and modulation of DNA-binding affects the rate of transcription complex formation and initiation of transcription. Mutations that expand the number of CAG repeats encoding this polyglutamine tract, and thus increase the length of the polyglutamine string, are associated with spinocerebellar ataxia 17, a neurodegenerative disorder classified as a polyglutamine disease.[12]

DNA-protein interactions

When TBP binds to a TATA box within the DNA, it distorts the DNA by inserting amino acid side-chains between base pairs, partially unwinding the helix, and doubly kinking it. The distortion is accomplished through a great amount of surface contact between the protein and DNA. TBP binds with the negatively charged phosphates in the DNA backbone through positively charged lysine and arginine amino acid residues. The sharp bend in the DNA is produced through projection of four bulky phenylalanine residues into the minor groove. As the DNA bends, its contact with TBP increases, thus enhancing the DNA-protein interaction.

The strain imposed on the DNA through this interaction initiates melting, or separation, of the strands. Because this region of DNA is rich in adenine and thymine residues, which base-pair through only two hydrogen bonds, the DNA strands are more easily separated. Separation of the two strands exposes the bases and allows RNA polymerase II to begin transcription of the gene.

TBP's C-terminus composes of a helicoidal shape that (incompletely) complements the T-A-T-A region of DNA. This incompleteness allows DNA to be passively bent on binding.

For information on the use of TBP in cells see: RNA polymerase I, RNA polymerase II, and RNA polymerase III.

Protein–protein interactions

TATA-binding protein has been shown to interact with:

Complex assembly

The TATA-box binding protein (TBP) is required for the initiation of transcription by RNA polymerases I, II and III, from promoters with or without a TATA box.[50][51] In the presence of a TATA-less promoter, TBP binds with the help of TBP-associated factors (TAFs).[52][53] TBP associates with a host of factors, including the general transcription factors TFIIA, -B, -D, -E, and -H, to form huge multi-subunit pre-initiation complexes on the core promoter. Through its association with different transcription factors, TBP can initiate transcription from different RNA polymerases. There are several related TBPs, including TBP-like (TBPL) proteins.[54]


The C-terminal core of TBP (~180 residues) is highly conserved and contains two 88-amino acid repeats that produce a saddle-shaped structure that straddles the DNA; this region binds to the TATA box and interacts with transcription factors and regulatory proteins .[55] By contrast, the N-terminal region varies in both length and sequence.


  1. ^ a b c GRCh38: Ensembl release 89: ENSG00000112592 - Ensembl, May 2017
  2. ^ "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  3. ^ "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  4. ^ Kornberg RD (2007). "The molecular basis of eukaryotic transcription". Proc. Natl. Acad. Sci. U.S.A. 104 (32): 12955–61. Bibcode:2007PNAS..10412955K. doi:10.1073/pnas.0704138104. PMC 1941834. PMID 17670940.
  5. ^ Akhtar W, Veenstra GJ (1 January 2011). "TBP-related factors: a paradigm of diversity in transcription initiation". Cell & Bioscience. 1 (1): 23. doi:10.1186/2045-3701-1-23. PMC 3142196. PMID 21711503.
  6. ^ Lee TI, Young RA (2000). "Transcription of eukaryotic protein-coding genes". Annual Review of Genetics. 34: 77–137. doi:10.1146/annurev.genet.34.1.77. PMID 11092823.
  7. ^ Lam KC, Mühlpfordt F, Vaquerizas JM, Raja SJ, Holz H, Luscombe NM, Manke T, Akhtar A (2012). "The NSL complex regulates housekeeping genes in Drosophila". PLOS Genetics. 8 (6): e1002736. doi:10.1371/journal.pgen.1002736. PMC 3375229. PMID 22723752.
  8. ^ a b Lam KC, Chung HR, Semplicio G, Iyer SS, Gaub A, Bhardwaj V, Holz H, Georgiev P, Akhtar A (February 2019). "The NSL complex-mediated nucleosome landscape is required to maintain transcription fidelity and suppression of transcription noise". Genes & Development. 33 (7–8): 452–465. doi:10.1101/gad.321489.118. PMC 6446542. PMID 30819819.
  9. ^ Carninci P, Sandelin A, Lenhard B, Katayama S, Shimokawa K, Ponjavic J, et al. (June 2006). "Genome-wide analysis of mammalian promoter architecture and evolution". Nature Genetics. 38 (6): 626–35. doi:10.1038/ng1789. PMID 16645617. S2CID 22205897.
  10. ^ Ni T, Corcoran DL, Rach EA, Song S, Spana EP, Gao Y, Ohler U, Zhu J (July 2010). "A paired-end sequencing strategy to map the complex landscape of transcription initiation". Nature Methods. 7 (7): 521–7. doi:10.1038/nmeth.1464. PMC 3197272. PMID 20495556.
  11. ^ Vannini A, Cramer P (February 2012). "Conservation between the RNA polymerase I, II, and III transcription initiation machineries". Molecular Cell. 45 (4): 439–46. doi:10.1016/j.molcel.2012.01.023. PMID 22365827.
  12. ^ "Entrez Gene: TBP TATA box binding protein".
  13. ^ McCulloch V, Hardin P, Peng W, Ruppert JM, Lobo-Ruppert SM (August 2000). "Alternatively spliced hBRF variants function at different RNA polymerase III promoters". EMBO J. 19 (15): 4134–43. doi:10.1093/emboj/19.15.4134. PMC 306597. PMID 10921893.
  14. ^ Wang Z, Roeder RG (July 1995). "Structure and function of a human transcription factor TFIIIB subunit that is evolutionarily conserved and contains both TFIIB- and high-mobility-group protein 2-related domains". Proc. Natl. Acad. Sci. U.S.A. 92 (15): 7026–30. Bibcode:1995PNAS...92.7026W. doi:10.1073/pnas.92.15.7026. PMC 41464. PMID 7624363.
  15. ^ a b c d Scully R, Anderson SF, Chao DM, Wei W, Ye L, Young RA, Livingston DM, Parvin JD (May 1997). "BRCA1 is a component of the RNA polymerase II holoenzyme". Proc. Natl. Acad. Sci. U.S.A. 94 (11): 5605–10. Bibcode:1997PNAS...94.5605S. doi:10.1073/pnas.94.11.5605. PMC 20825. PMID 9159119.
  16. ^ Chicca JJ, Auble DT, Pugh BF (March 1998). "Cloning and biochemical characterization of TAF-172, a human homolog of yeast Mot1". Mol. Cell. Biol. 18 (3): 1701–10. doi:10.1128/MCB.18.3.1701. PMC 108885. PMID 9488487.
  17. ^ Metz R, Bannister AJ, Sutherland JA, Hagemeier C, O'Rourke EC, Cook A, Bravo R, Kouzarides T (September 1994). "c-Fos-induced activation of a TATA-box-containing promoter involves direct contact with TATA-box-binding protein". Mol. Cell. Biol. 14 (9): 6021–9. doi:10.1128/MCB.14.9.6021. PMC 359128. PMID 8065335.
  18. ^ Franklin CC, McCulloch AV, Kraft AS (February 1995). "In vitro association between the Jun protein family and the general transcription factors, TBP and TFIIB". Biochem. J. 305 (3): 967–74. doi:10.1042/bj3050967. PMC 1136352. PMID 7848298.
  19. ^ Brendel C, Gelman L, Auwerx J (June 2002). "Multiprotein bridging factor-1 (MBF-1) is a cofactor for nuclear receptors that regulate lipid metabolism". Mol. Endocrinol. 16 (6): 1367–77. doi:10.1210/mend.16.6.0843. PMID 12040021.
  20. ^ Mariotti M, De Benedictis L, Avon E, Maier JA (August 2000). "Interaction between endothelial differentiation-related factor-1 and calmodulin in vitro and in vivo". J. Biol. Chem. 275 (31): 24047–51. doi:10.1074/jbc.M001928200. PMID 10816571.
  21. ^ Kabe Y, Goto M, Shima D, Imai T, Wada T, Morohashi Ki, Shirakawa M, Hirose S, Handa H (November 1999). "The role of human MBF1 as a transcriptional coactivator". J. Biol. Chem. 274 (48): 34196–202. doi:10.1074/jbc.274.48.34196. PMID 10567391.
  22. ^ a b Tang H, Sun X, Reinberg D, Ebright RH (February 1996). "Protein–protein interactions in eukaryotic transcription initiation: structure of the preinitiation complex". Proc. Natl. Acad. Sci. U.S.A. 93 (3): 1119–24. Bibcode:1996PNAS...93.1119T. doi:10.1073/pnas.93.3.1119. PMC 40041. PMID 8577725.CS1 maint: uses authors parameter (link)
  23. ^ Bushnell DA, Westover KD, Davis RE, Kornberg RD (February 2004). "Structural basis of transcription: an RNA polymerase II-TFIIB cocrystal at 4.5 Angstroms". Science. 303 (5660): 983–8. Bibcode:2004Sci...303..983B. doi:10.1126/science.1090838. PMID 14963322. S2CID 36598301.
  24. ^ DeJong J, Bernstein R, Roeder RG (April 1995). "Human general transcription factor TFIIA: characterization of a cDNA encoding the small subunit and requirement for basal and activated transcription". Proc. Natl. Acad. Sci. U.S.A. 92 (8): 3313–7. Bibcode:1995PNAS...92.3313D. doi:10.1073/pnas.92.8.3313. PMC 42156. PMID 7724559.
  25. ^ Ozer J, Mitsouras K, Zerby D, Carey M, Lieberman PM (June 1998). "Transcription factor IIA derepresses TATA-binding protein (TBP)-associated factor inhibition of TBP-DNA binding". J. Biol. Chem. 273 (23): 14293–300. doi:10.1074/jbc.273.23.14293. PMID 9603936.
  26. ^ Sun X, Ma D, Sheldon M, Yeung K, Reinberg D (October 1994). "Reconstitution of human TFIIA activity from recombinant polypeptides: a role in TFIID-mediated transcription". Genes Dev. 8 (19): 2336–48. doi:10.1101/gad.8.19.2336. PMID 7958900.
  27. ^ Ruppert S, Tjian R (November 1995). "Human TAFII250 interacts with RAP74: implications for RNA polymerase II initiation". Genes Dev. 9 (22): 2747–55. doi:10.1101/gad.9.22.2747. PMID 7590250.
  28. ^ Malik S, Guermah M, Roeder RG (March 1998). "A dynamic model for PC4 coactivator function in RNA polymerase II transcription". Proc. Natl. Acad. Sci. U.S.A. 95 (5): 2192–7. Bibcode:1998PNAS...95.2192M. doi:10.1073/pnas.95.5.2192. PMC 19292. PMID 9482861.
  29. ^ Thut CJ, Goodrich JA, Tjian R (August 1997). "Repression of p53-mediated transcription by MDM2: a dual mechanism". Genes Dev. 11 (15): 1974–86. doi:10.1101/gad.11.15.1974. PMC 316412. PMID 9271120.
  30. ^ Léveillard T, Wasylyk B (December 1997). "The MDM2 C-terminal region binds to TAFII250 and is required for MDM2 regulation of the cyclin A promoter". J. Biol. Chem. 272 (49): 30651–61. doi:10.1074/jbc.272.49.30651. PMID 9388200.
  31. ^ Shetty S, Takahashi T, Matsui H, Ayengar R, Raghow R (May 1999). "Transcriptional autorepression of Msx1 gene is mediated by interactions of Msx1 protein with a multi-protein transcriptional complex containing TATA-binding protein, Sp1 and cAMP-response-element-binding protein-binding protein (CBP/p300)". Biochem. J. 339 (3): 751–8. doi:10.1042/0264-6021:3390751. PMC 1220213. PMID 10215616.
  32. ^ Zhang H, Hu G, Wang H, Sciavolino P, Iler N, Shen MM, Abate-Shen C (May 1997). "Heterodimerization of Msx and Dlx homeoproteins results in functional antagonism". Mol. Cell. Biol. 17 (5): 2920–32. doi:10.1128/mcb.17.5.2920. PMC 232144. PMID 9111364.
  33. ^ Zhang H, Catron KM, Abate-Shen C (March 1996). "A role for the Msx-1 homeodomain in transcriptional regulation: residues in the N-terminal arm mediate TATA binding protein interaction and transcriptional repression". Proc. Natl. Acad. Sci. U.S.A. 93 (5): 1764–9. Bibcode:1996PNAS...93.1764Z. doi:10.1073/pnas.93.5.1764. PMC 39855. PMID 8700832.
  34. ^ a b c d e f g h Bellorini M, Lee DK, Dantonel JC, Zemzoumi K, Roeder RG, Tora L, Mantovani R (June 1997). "CCAAT binding NF-Y-TBP interactions: NF-YB and NF-YC require short domains adjacent to their histone fold motifs for association with TBP basic residues". Nucleic Acids Res. 25 (11): 2174–81. doi:10.1093/nar/25.11.2174. PMC 146709. PMID 9153318.
  35. ^ Seto E, Usheva A, Zambetti GP, Momand J, Horikoshi N, Weinmann R, Levine AJ, Shenk T (December 1992). "Wild-type p53 binds to the TATA-binding protein and represses transcription". Proc. Natl. Acad. Sci. U.S.A. 89 (24): 12028–32. Bibcode:1992PNAS...8912028S. doi:10.1073/pnas.89.24.12028. PMC 50691. PMID 1465435.
  36. ^ a b Cvekl A, Kashanchi F, Brady JN, Piatigorsky J (June 1999). "Pax-6 interactions with TATA-box-binding protein and retinoblastoma protein". Invest. Ophthalmol. Vis. Sci. 40 (7): 1343–50. PMID 10359315.
  37. ^ Zwilling S, Annweiler A, Wirth T (May 1994). "The POU domains of the Oct1 and Oct2 transcription factors mediate specific interaction with TBP". Nucleic Acids Res. 22 (9): 1655–62. doi:10.1093/nar/22.9.1655. PMC 308045. PMID 8202368.
  38. ^ Guermah M, Malik S, Roeder RG (June 1998). "Involvement of TFIID and USA components in transcriptional activation of the human immunodeficiency virus promoter by NF-kappaB and Sp1". Mol. Cell. Biol. 18 (6): 3234–44. doi:10.1128/mcb.18.6.3234. PMC 108905. PMID 9584164.
  39. ^ Schmitz ML, Stelzer G, Altmann H, Meisterernst M, Baeuerle PA (March 1995). "Interaction of the COOH-terminal transactivation domain of p65 NF-kappa B with TATA-binding protein, transcription factor IIB, and coactivators". J. Biol. Chem. 270 (13): 7219–26. doi:10.1074/jbc.270.13.7219. PMID 7706261.
  40. ^ Schulman IG, Chakravarti D, Juguilon H, Romo A, Evans RM (August 1995). "Interactions between the retinoid X receptor and a conserved region of the TATA-binding protein mediate hormone-dependent transactivation". Proc. Natl. Acad. Sci. U.S.A. 92 (18): 8288–92. Bibcode:1995PNAS...92.8288S. doi:10.1073/pnas.92.18.8288. PMC 41142. PMID 7667283.
  41. ^ Siegert JL, Robbins PD (January 1999). "Rb inhibits the intrinsic kinase activity of TATA-binding protein-associated factor TAFII250". Mol. Cell. Biol. 19 (1): 846–54. doi:10.1128/MCB.19.1.846. PMC 83941. PMID 9858607.
  42. ^ a b c d Ruppert S, Wang EH, Tjian R (March 1993). "Cloning and expression of human TAFII250: a TBP-associated factor implicated in cell-cycle regulation". Nature. 362 (6416): 175–9. Bibcode:1993Natur.362..175R. doi:10.1038/362175a0. PMID 7680771. S2CID 4364676.
  43. ^ O'Brien T, Tjian R (May 1998). "Functional analysis of the human TAFII250 N-terminal kinase domain". Mol. Cell. 1 (6): 905–11. doi:10.1016/S1097-2765(00)80089-1. PMID 9660973.
  44. ^ a b c Pointud JC, Mengus G, Brancorsini S, Monaco L, Parvinen M, Sassone-Corsi P, Davidson I (May 2003). "The intracellular localisation of TAF7L, a paralogue of transcription factor TFIID subunit TAF7, is developmentally regulated during male germ-cell differentiation". J. Cell Sci. 116 (Pt 9): 1847–58. doi:10.1242/jcs.00391. PMID 12665565.
  45. ^ Tao Y, Guermah M, Martinez E, Oelgeschläger T, Hasegawa S, Takada R, Yamamoto T, Horikoshi M, Roeder RG (March 1997). "Specific interactions and potential functions of human TAFII100". J. Biol. Chem. 272 (10): 6714–21. doi:10.1074/jbc.272.10.6714. PMID 9045704.
  46. ^ Martinez E, Palhan VB, Tjernberg A, Lymar ES, Gamper AM, Kundu TK, Chait BT, Roeder RG (October 2001). "Human STAGA complex is a chromatin-acetylating transcription coactivator that interacts with pre-mRNA splicing and DNA damage-binding factors in vivo". Mol. Cell. Biol. 21 (20): 6782–95. doi:10.1128/MCB.21.20.6782-6795.2001. PMC 99856. PMID 11564863.
  47. ^ a b Mengus G, May M, Jacq X, Staub A, Tora L, Chambon P, Davidson I (April 1995). "Cloning and characterization of hTAFII18, hTAFII20 and hTAFII28: three subunits of the human transcription factor TFIID". EMBO J. 14 (7): 1520–31. doi:10.1002/j.1460-2075.1995.tb07138.x. PMC 398239. PMID 7729427.
  48. ^ May M, Mengus G, Lavigne AC, Chambon P, Davidson I (June 1996). "Human TAF(II28) promotes transcriptional stimulation by activation function 2 of the retinoid X receptors". EMBO J. 15 (12): 3093–104. doi:10.1002/j.1460-2075.1996.tb00672.x. PMC 450252. PMID 8670810.
  49. ^ Hoffmann A, Roeder RG (July 1996). "Cloning and characterization of human TAF20/15. Multiple interactions suggest a central role in TFIID complex formation". J. Biol. Chem. 271 (30): 18194–202. doi:10.1074/jbc.271.30.18194. PMID 8663456.
  50. ^ Hochheimer A, Tjian R (June 2003). "Diversified transcription initiation complexes expand promoter selectivity and tissue-specific gene expression". Genes & Development. 17 (11): 1309–20. doi:10.1101/gad.1099903. PMID 12782648.
  51. ^ Pugh BF (September 2000). "Control of gene expression through regulation of the TATA-binding protein". Gene. 255 (1): 1–14. doi:10.1016/s0378-1119(00)00288-2. PMID 10974559.
  52. ^ 1942-, Weaver, Robert Franklin (1 January 2012). Molecular biology. McGraw-Hill. ISBN 9780073525327. OCLC 789601172.CS1 maint: numeric names: authors list (link)
  53. ^ Louder RK, He Y, López-Blanco JR, Fang J, Chacón P, Nogales E (March 2016). "Structure of promoter-bound TFIID and model of human pre-initiation complex assembly". Nature. 531 (7596): 604–9. Bibcode:2016Natur.531..604L. doi:10.1038/nature17394. PMC 4856295. PMID 27007846.
  54. ^ Davidson I (July 2003). "The genetics of TBP and TBP-related factors". Trends in Biochemical Sciences. 28 (7): 391–8. doi:10.1016/S0968-0004(03)00117-8. PMID 12878007.
  55. ^ Nikolov DB, Hu SH, Lin J, Gasch A, Hoffmann A, Horikoshi M, Chua NH, Roeder RG, Burley SK (November 1992). "Crystal structure of TFIID TATA-box binding protein". Nature. 360 (6399): 40–6. Bibcode:1992Natur.360...40N. doi:10.1038/360040a0. PMID 1436073. S2CID 4307043.

External links

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Transcription factor TFIID (or TATA-binding protein, TBP) Provide feedback

No Pfam abstract.

Literature references

  1. Nikolov DB, Hu SH, Lin J, Gasch A, Hoffmann A, Horikoshi M, Chua NH, Roeder RG, Burley SK; , Nature 1992;360:40-46.: Crystal structure of TFIID TATA-box binding protein. PUBMED:1436073 EPMC:1436073

  2. Hoffmann A, Chiang CM, Oelgeschlager T, Xie X, Burley SK, Nakatani Y, Roeder RG; , Nature 1996;380:356-359.: A histone octamer-like structure within TFIID. PUBMED:8598932 EPMC:8598932

  3. Hoffman A, Sinn E, Yamamoto T, Wang J, Roy A, Horikoshi M, Roeder RG; , Nature 1990;346:387-390.: Highly conserved core domain and unique N terminus with presumptive regulatory motifs in a human TATA factor (TFIID). PUBMED:2374612 EPMC:2374612

  4. Gasch A, Hoffmann A, Horikoshi M, Roeder RG, Chua NH; , Nature 1990;346:390-394.: Arabidopsis thaliana contains two genes for TFIID. PUBMED:2197561 EPMC:2197561

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000814

The TATA-box binding protein (TBP) is required for the initiation of transcription by RNA polymerases I, II and III, from promoters with or without a TATA box [ PUBMED:12782648 , PUBMED:10974559 ]. TBP associates with a host of factors, including the general transcription factors SL1, TFIIA, -B, -D, -E, and -H, to form huge multi-subunit pre-initiation complexes on the core promoter. Through its association with different transcription factors, TBP can initiate transcription from different RNA polymerases. There are several related TBPs, including TBP-like (TBPL) proteins [ PUBMED:12878007 ]. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site.

The C-terminal core of TBP (~180 residues) is highly conserved and contains two 77-amino acid repeats that produce a saddle-shaped structure that straddles the DNA; this region binds to the TATA box and interacts with transcription factors and regulatory proteins [ PUBMED:1436073 ]. By contrast, the N-terminal region varies in both length and sequence.

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

Loading domain graphics...

Pfam Clan

This family is a member of clan TBP-like (CL0407), which has the following description:

TBP is a transcription factor whose DNA binding fold is composed of a curved antiparallel beta-sheet [1]. This fold is also found in the N terminal region of DNA repair glycosylases. The N terminal domain of DNA glycosylase has only a single copy of the fold, whereas TBP contains a duplication of this fold [2-3].

The clan contains the following 10 members:

AdoMet_dc AlkA_N DUF3378 DUF5611 OGG_N Phage_CRI Rep_trans Rol_Rep_N SpmSyn_N TBP


We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

View options

We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

Representative proteomes UniProt
Jalview View  View  View  View  View  View  View 
HTML View             
PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

Representative proteomes UniProt

Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

Representative proteomes UniProt
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...


This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Prosite
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Finn RD
Number in seed: 274
Number in full: 7937
Average length of the domain: 80.80 aa
Average identity of full alignment: 40 %
Average coverage of the sequence by the domain: 59.06 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.9 22.9
Trusted cut-off 22.9 22.9
Noise cut-off 22.8 22.8
Model length: 85
Family (HMM) version: 24
Download: download the raw HMM for this family

Species distribution

Sunburst controls


Weight segments by...

Change the size of the sunburst


Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence


Align selected sequences to HMM

Generate a FASTA-format file

Clear selection

This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

Loading sunburst data...

Tree controls


The tree shows the occurrence of this domain across different species. More...


Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.


For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the TBP domain has been found. There are 302 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

Loading structure mapping...

AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A0R0KSZ8 View 3D Structure Click here
A0A144A3A5 View 3D Structure Click here
A0A1D6GMS0 View 3D Structure Click here
A0A1D6HZ79 View 3D Structure Click here
A0A1D6JMK1 View 3D Structure Click here
A0A1D6K7I2 View 3D Structure Click here
A0A368UIM7 View 3D Structure Click here
A0B5H8 View 3D Structure Click here
A4HYG9 View 3D Structure Click here
A6H907 View 3D Structure Click here
A6H909 View 3D Structure Click here
A6UTF6 View 3D Structure Click here
A7UFC2 View 3D Structure Click here
B2D6P4 View 3D Structure Click here
C4M7H7 View 3D Structure Click here
C6A0R1 View 3D Structure Click here
D4A898 View 3D Structure Click here
D4GZA2 View 3D Structure Click here
D4H071 View 3D Structure Click here
I1L726 View 3D Structure Click here
I1N371 View 3D Structure Click here
O13270 View 3D Structure Click here
O27664 View 3D Structure Click here
O29874 View 3D Structure Click here
O43133 View 3D Structure Click here
O45211 View 3D Structure Click here
O52004 View 3D Structure Click here
O52018 View 3D Structure Click here
O74045 View 3D Structure Click here
P13393 View 3D Structure Click here
P17871 View 3D Structure Click here
P20226 View 3D Structure Click here
P20227 View 3D Structure Click here
P26355 View 3D Structure Click here
P26356 View 3D Structure Click here
P26357 View 3D Structure Click here
P28147 View 3D Structure Click here
P28148 View 3D Structure Click here
P29037 View 3D Structure Click here
P32085 View 3D Structure Click here