Summary: Transcription initiation factor IID, 18kD subunit
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This is the Wikipedia entry entitled "TBP-associated factor". More...
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TBP-associated factor Edit Wikipedia article
|TBP associated factor (TAF6)|
|SCOP2||1bh9 / SCOPe / SUPFAM|
The TBP-associated factors (TAF) are proteins that associate with the TATA-binding protein in transcription initiation. It is a part of the transcription initiation factor TFIID multimeric protein complex. It also makes up many other factors, including SL1. They mediate the formation of the transcription preinitiation complex, a step preceding transcription of DNA to RNA by RNA polymerase II.
TFIID plays a central role in mediating promoter responses to various activators and repressors. It binds tightly to TAFII-250 and directly interacts with TAFII-40. TFIID is composed of TATA binding protein (TBP) and a number of TBP-associated factors (TAFS).
TAF is part of the TFIID complex, and interacts with the following:
- Specific transcriptional activators
- Basal transcription factors
- Other TAFIIs
- Specific DNA sequences, for example the downstream promoter element or gene-specific core promoter sequence
Due to such interactions, they contribute transcription activation and to promoter selectivity.
Some pairs of TAF interact with each other to form "lobes" in TFIID. Pairs known or suggested to exist in TFIID include TAF6-TAF9, TAF4-TAF12, TAF11-13, TAF8-TAF10 and TAF3-TAF10.
Selective factor 1 is composed of the TATA-binding protein and three TAF (TATA box-binding protein-associated factor) subunits (TAF1A, TAF1B, and TAF1C). These TAFs do not have a histone-like fold domain.
This section is missing information about subunits of SAGA and related complexes, and pair-forming therein.(April 2019)
TAF is a part of SAGA (SPT-ADA-GCN5 acetylase) and related coactivation complexes. Such complexes acetylate histone tails to activate genes. Human has three SAGA-like complexes: PCAF, TFTC (TBP-free TAF-containing complex), and STAGA (SPT3-TAF9-GCN5L acetylase). PCAF (GCN5) and KAT2A (GCN5L) are two human homologs of the yeast Gcn5.
This section is missing information about TAFs in non-TF2D complexes.(April 2019)
- TAF1 (TAFII250)
- TAF2 (CIF150)
- TAF3 (TAFII140)
- TAF4 (TAFII130/135)
- TAF4B (TAFII105)
- TAF5 (TAFII100)
- TAF6 (TAFII70/80)
- TAF6L (PAF65A)
- TAF7 (TAFII55)
- TAF8 (TAFII43)
- TAF9 (TAFII31/32)
- TAF9B (TAFII31L)
- TAF10 (TAFII30)
- TAF11 (TAFII28)
- TAF12 (TAFII20/15)
- TAF13 (TAFII18)
- TAF15 (TAFII68)
TAF domains are spread out across many digital signatures:
- Xie X, Kokubo T, Cohen SL, Mirza UA, Hoffmann A, Chait BT, Roeder RG, Nakatani Y, Burley SK (March 1996). "Structural similarity between TAFs and the heterotetrameric core of the histone octamer". Nature. 380 (6572): 316â€“22. Bibcode:1996Natur.380..316X. doi:10.1038/380316a0. PMIDÂ 8598927. S2CIDÂ 4329570.
- DemÃ©ny MA, Soutoglou E, Nagy Z, Scheer E, JÃ noshÃ zi A, Richardot M, Argentini M, Kessler P, Tora L (March 2007). "Identification of a small TAF complex and its role in the assembly of TAF-containing complexes". PLOS ONE. 2 (3): e316. Bibcode:2007PLoSO...2..316D. doi:10.1371/journal.pone.0000316. PMCÂ 1820849. PMIDÂ 17375202.
- Furukawa T, Tanese N (September 2000). "Assembly of partial TFIID complexes in mammalian cells reveals distinct activities associated with individual TATA box-binding protein-associated factors". The Journal of Biological Chemistry. 275 (38): 29847â€“56. doi:10.1074/jbc.M002989200. PMIDÂ 10896937.
- Friedrich JK, Panov KI, Cabart P, Russell J, Zomerdijk JC (August 2005). "TBP-TAF complex SL1 directs RNA polymerase I pre-initiation complex formation and stabilizes upstream binding factor at the rDNA promoter". The Journal of Biological Chemistry. 280 (33): 29551â€“8. doi:10.1074/jbc.M501595200. PMCÂ 3858828. PMIDÂ 15970593.
- Bonnet J, Wang CY, Baptista T, Vincent SD, Hsiao WC, Stierle M, Kao CF, Tora L, Devys D (September 2014). "The SAGA coactivator complex acts on the whole transcribed genome and is required for RNA polymerase II transcription". Genes & Development. 28 (18): 1999â€“2012. doi:10.1101/gad.250225.114. PMCÂ 4173158. PMIDÂ 25228644.
- 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". Molecular and Cellular Biology. 21 (20): 6782â€“95. doi:10.1128/MCB.21.20.6782-6795.2001. PMCÂ 99856. PMIDÂ 11564863.
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Transcription initiation factor IID, 18kD subunit Provide feedback
This family includes the Spt3 yeast transcription factors and the 18kD subunit from human transcription initiation factor IID (TFIID-18). Determination of the crystal structure reveals an atypical histone fold 
Birck C, Poch O, Romier C, Ruff M, Mengus G, Lavigne AC, Davidson I, Moras D; , Cell 1998;94:239-249.: Human TAF(II)28 and TAF(II)18 interact through a histone fold encoded by atypical evolutionary conserved motifs also found in the SPT3 family. PUBMED:9695952 EPMC:9695952
Internal database links
|SCOOP:||Bromo_TP CBFD_NFYB_HMF CENP-S CENP-T_C Histone TFIID_20kDa|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR003195
This family includes the Spt3 yeast transcription factors and the 18kDa subunit from human transcription initiation factor IID, known as TAF13 or TAFII18. Determination of the crystal structure reveals an atypical histone fold [ PUBMED:9695952 ].
TBP-associated factor 13 (TAF13) is one of several TAFs that bind TBP and is involved in forming the transcription factor IID (TFIID) complex. TAF13 interacts with TAF11 and makes a histone-like heterodimer similar to H3/H4-like proteins. The dimer may be structurally and functionally similar to the spt3 protein within the SAGA histone acetyltransferase complex [ PUBMED:9695952 ].
TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. Each TAF, with the help of a specific activator, is required only for expression of subset of genes and is not universally involved for transcription as are GTFs. In yeast and human cells, TAFs have been found as components of other complexes besides TFIID. Several TAFs interact via histone-fold (HFD) motifs; the HFD is the interaction motif involved in heterodimerization of the core histones and their assembly into nucleosome octamers. The minimal HFD contains three alpha-helices linked by two loops and are found in core histones, TAFs and many other transcription factors. TFIID has a histone octamer-like substructure.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Biological process||transcription by RNA polymerase II (GO:0006366)|
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Members of this clan all possess a histone fold. Generally proteins in this clan are DNA binding.
The clan contains the following 17 members:Bromo_TP Bromo_TP_like CBFD_NFYB_HMF CENP-S CENP-T_C CENP-W CENP-X DUF1931 Histone PAF TAF TAF4 TAFII28 TFIID-18kDa TFIID-31kDa TFIID_20kDa TFIID_30kDa
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
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|Seed source:||Pfam-B_3681 (release 5.2)|
|Author:||Bateman A , Mian N|
|Number in seed:||6|
|Number in full:||3054|
|Average length of the domain:||88.20 aa|
|Average identity of full alignment:||35 %|
|Average coverage of the sequence by the domain:||33.62 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||19|
|Download:||download the raw HMM for this family|
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For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.
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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 TFIID-18kDa domain has been found. There are 22 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.
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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|
|A0A0R4IR35||View 3D Structure||Click here|
|A0A1D6MST2||View 3D Structure||Click here|
|A0A1D8PR78||View 3D Structure||Click here|
|A0A1D8PU74||View 3D Structure||Click here|
|B2RYQ7||View 3D Structure||Click here|
|B9EW84||View 3D Structure||Click here|
|C6T027||View 3D Structure||Click here|
|C6TAB5||View 3D Structure||Click here|
|F1LY08||View 3D Structure||Click here|
|F1QBH2||View 3D Structure||Click here|
|I1L7R2||View 3D Structure||Click here|
|O13472||View 3D Structure||Click here|
|O14311||View 3D Structure||Click here|
|O60076||View 3D Structure||Click here|
|O75486||View 3D Structure||Click here|
|P06844||View 3D Structure||Click here|
|P11747||View 3D Structure||Click here|
|P61216||View 3D Structure||Click here|
|Q148M7||View 3D Structure||Click here|
|Q15543||View 3D Structure||Click here|
|Q17957||View 3D Structure||Click here|
|Q54CN8||View 3D Structure||Click here|
|Q5R9W6||View 3D Structure||Click here|
|Q6NQH4||View 3D Structure||Click here|
|Q8BVY4||View 3D Structure||Click here|
|Q9VGE2||View 3D Structure||Click here|
|Q9VIP1||View 3D Structure||Click here|