Summary: TATA box binding protein associated factor (TAF)
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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.
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.
TATA box binding protein associated factor (TAF) Provide feedback
TAF proteins adopt a histone-like fold.
Xie X, Kokubo T, Cohen SL, Mirza UA, Hoffmann A, Chait BT, Roeder RG, Nakatani Y, Burley SK; , Nature 1996;380:316-322.: Structural similarity between TAFs and the heterotetrameric core of the histone octamer. PUBMED:8598927 EPMC:8598927
Internal database links
|SCOOP:||Bromo_TP CBFD_NFYB_HMF CENP-S CENP-T_C Histone TFIID-31kDa TFIID_20kDa|
|Similarity to PfamA using HHSearch:||Histone CBFD_NFYB_HMF CENP-S|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR004823
The TATA box binding protein associated factor (TAF) is part of the transcription initiation factor TFIID multimeric protein complex. 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 proteins adopt a histone-like fold.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Biological process||DNA-templated transcription, initiation (GO:0006352)|
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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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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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.
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|Seed source:||Structural domain|
|Number in seed:||8|
|Number in full:||2444|
|Average length of the domain:||64.50 aa|
|Average identity of full alignment:||39 %|
|Average coverage of the sequence by the domain:||13.01 %|
|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:||20|
|Download:||download the raw HMM for this family|
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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the More....
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How the sunburst is generated
The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.
In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:
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Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.
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Unmapped species names
The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
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Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
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For large species trees, you may see blank regions in the outer layers of the sunburst. These occur when there are large numbers of arcs to be drawn in a small space. If an arc is less than approximately one pixel wide, it will not be drawn and the space will be left blank. You may still be able to get some information about the species in that region by moving your mouse across the area, but since each arc will be very small, it will be difficult to accurately locate a particular species.
The tree shows the occurrence of this domain across different species. More...
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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.
We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.
Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.
We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.
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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 TAF domain has been found. There are 43 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|
|A0A0R0EY64||View 3D Structure||Click here|
|A0A0R0J477||View 3D Structure||Click here|
|A0A1D8PKJ2||View 3D Structure||Click here|
|B5DF37||View 3D Structure||Click here|
|B8A2G2||View 3D Structure||Click here|
|E7FEV1||View 3D Structure||Click here|
|F4HVA6||View 3D Structure||Click here|
|I1JDP3||View 3D Structure||Click here|
|O74462||View 3D Structure||Click here|
|P49847||View 3D Structure||Click here|
|P49848||View 3D Structure||Click here|
|P53040||View 3D Structure||Click here|
|P91849||View 3D Structure||Click here|
|Q54IW7||View 3D Structure||Click here|
|Q62311||View 3D Structure||Click here|
|Q63801||View 3D Structure||Click here|
|Q66HZ5||View 3D Structure||Click here|
|Q8LRG9||View 3D Structure||Click here|
|Q8R2K4||View 3D Structure||Click here|
|Q9GZI6||View 3D Structure||Click here|
|Q9MAU3||View 3D Structure||Click here|
|Q9Y6J9||View 3D Structure||Click here|