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40  structures 1405  species 0  interactions 2120  sequences 41  architectures

Family: TFIID_20kDa (PF03847)

Summary: Transcription initiation factor TFIID subunit A

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 "TBP-associated factor". More...

TBP-associated factor Edit Wikipedia article

TAF
PDB 1taf EBI.jpg
drosophila tbp associated factors dtafii42/dtafii62 heterotetramer
Identifiers
SymbolTAF
PfamPF02969
Pfam clanCL0012
InterProIPR004823
SMARTTAFH
SCOP21bh9 / SCOPe / SUPFAM

In molecular biology, this entry, TAF refers to a protein named the TATA box binding protein associated factor. TAF is part of the transcription initiation factor TFIID multimeric protein complex, or in simpler terms, the Pre-initiation complex (PIC). TAF forms part of Transcription factor II D (TFIID) and the TATA-binding protein (TBP). They mediate transcription of DNA to RNA by RNA PolymeraseRNA polymerase II. This entry discusses the N-terminal domain in particular.

TFIID

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)[1]. TAF proteins adopt a histone-like fold.

TAF function

There are several function of TAF in its role as part of the TFIID complex, their function is to interact 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 therefore contribute transcription activation and to promoter selectivity. [1]

TAF structure

The N-terminal domain of TAF has a histone-like protein fold. It contains two short alpha helices and a long central alpha helix. [2]

Types of TAF

References

  1. ^ a b Furukawa T, Tanese N (2000). "Assembly of partial TFIID complexes in mammalian cells reveals distinct activities associated with individual TATA box-binding protein-associated factors". J Biol Chem. 275 (38): 29847–56. doi:10.1074/jbc.M002989200. PMID 10896937.
  2. ^ Xie X, Kokubo T, Cohen SL, Mirza UA, Hoffmann A, Chait BT; et al. (1996). "Structural similarity between TAFs and the heterotetrameric core of the histone octamer". Nature. 380 (6572): 316–22. doi:10.1038/380316a0. PMID 8598927. {{cite journal}}: Explicit use of et al. in: |author= (help)CS1 maint: multiple names: authors list (link)
This article incorporates text from the public domain Pfam and InterPro: IPR004823

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 initiation factor TFIID subunit A Provide feedback

No Pfam abstract.

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR003228

TFIID is one of several General Transcription Factors (GTFs), which also include TFIIA, TFIIB, TFIIE, TFIIF and TFIIH, that are involved in the 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. Human transcription initiation factor TFIID is composed of the TATA-binding protein (TBP) and at least 13 TBP-associated factors (TAFs) that collectively or individually are involved in activator-dependent transcription [ PUBMED:7667268 , PUBMED:10664584 ].

TBP-associated factor 12 (TAF12) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TAF12 interacts with TAF4 and makes a novel histone-like heterodimer that binds DNA and has a core promoter function of a subset of genes [ PUBMED:19635797 ].

This entry represents a domain found in TAF12.

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...

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Pfam Clan

This family is a member of clan Histone (CL0012), which has the following description:

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

Alignments

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...

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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.

  Seed
(8)
Full
(2120)
Representative proteomes UniProt
(3386)
RP15
(429)
RP35
(1014)
RP55
(1656)
RP75
(2198)
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PP/heatmap 1 View           

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

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

Format an alignment

  Seed
(8)
Full
(2120)
Representative proteomes UniProt
(3386)
RP15
(429)
RP35
(1014)
RP55
(1656)
RP75
(2198)
Alignment:
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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.

  Seed
(8)
Full
(2120)
Representative proteomes UniProt
(3386)
RP15
(429)
RP35
(1014)
RP55
(1656)
RP75
(2198)
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...

Trees

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: PRODOM
Previous IDs: TFIID_A;
Type: Domain
Sequence Ontology: SO:0000417
Author: Griffiths-Jones SR
Number in seed: 8
Number in full: 2120
Average length of the domain: 68.1 aa
Average identity of full alignment: 47 %
Average coverage of the sequence by the domain: 15.62 %

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 27.0 27.0
Trusted cut-off 27.0 27.0
Noise cut-off 26.9 26.9
Model length: 68
Family (HMM) version: 16
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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Structures

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_20kDa domain has been found. There are 40 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
A0A044TVM4 View 3D Structure Click here
A0A077YXB8 View 3D Structure Click here
A0A0D2GQL6 View 3D Structure Click here
A0A0G2JZ70 View 3D Structure Click here
A0A0K0DUB7 View 3D Structure Click here
A0A0K0J1G6 View 3D Structure Click here
A0A0N4U6T0 View 3D Structure Click here
A0A0N4U7S7 View 3D Structure Click here
A0A0R0FJI2 View 3D Structure Click here
A0A175VVK3 View 3D Structure Click here
A0A175VXS1 View 3D Structure Click here
A0A1C1CR39 View 3D Structure Click here
A0A1D6N6Q8 View 3D Structure Click here
A0A1D6N779 View 3D Structure Click here
A0A1D8PSN1 View 3D Structure Click here
A0A1P6BG08 View 3D Structure Click here
A0A3P7E0G3 View 3D Structure Click here
A0A3P7EMY3 View 3D Structure Click here
C1H5C3 View 3D Structure Click here
G4LWN5 View 3D Structure Click here
I1KHA5 View 3D Structure Click here
I1L9B8 View 3D Structure Click here
I1LZI7 View 3D Structure Click here
K7VNK4 View 3D Structure Click here
O13722 View 3D Structure Click here
P49905 View 3D Structure Click here
Q03761 View 3D Structure Click here
Q0JHK4 View 3D Structure Click here
Q16514 View 3D Structure Click here
Q3T174 View 3D Structure Click here
Q555L9 View 3D Structure Click here
Q5ADM2 View 3D Structure Click here
Q5N796 View 3D Structure Click here
Q6P013 View 3D Structure Click here
Q8VE65 View 3D Structure Click here
Q940A7 View 3D Structure Click here
Q9SR71 View 3D Structure Click here
Q9U226 View 3D Structure Click here
Q9VR21 View 3D Structure Click here
U7Q7H5 View 3D Structure Click here