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4  structures 277  species 0  interactions 357  sequences 7  architectures

Family: TFIIA_gamma_C (PF02751)

Summary: Transcription initiation factor IIA, gamma subunit

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Transcription initiation factor IIA, gamma subunit Provide feedback

Accurate transcription in vivo requires at least six general transcription initiation factors, in addition to RNA polymerase II. Transcription initiation factor IIA (TFIIA) is a multimeric protein which facilitates the binding of TFIID to the TATA box. The C-terminal domain of the gamma subunit is a 12 stranded beta-barrel.

Literature references

  1. DeJong J, Bernstein R, Roeder RG; , Proc Natl Acad Sci U S A 1995;92:3313-3317.: Human general transcription factor TFIIA: characterization of a cDNA encoding the small subunit and requirement for basal and activated transcription. PUBMED:7724559 EPMC:7724559

  2. Tan S, Hunziker Y, Sargent DF, Richmond TJ; , Nature 1996;381:127-151.: Crystal structure of a yeast TFIIA/TBP/DNA complex. PUBMED:8610010 EPMC:8610010


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR015871

Transcription factor IIA (TFIIA) is one of several factors that form part of a transcription pre-initiation complex along with RNA polymerase II, the TATA-box-binding protein (TBP) and TBP-associated factors, on the TATA-box sequence upstream of the initiation start site. After initiation, some components of the pre-initiation complex (including TFIIA) remain attached and re-initiate a subsequent round of transcription. TFIIA binds to TBP to stabilise TBP binding to the TATA element. TFIIA also inhibits the cytokine HMGB1 (high mobility group 1 protein) binding to TBP [PUBMED:12818428], and can dissociate HMGB1 already bound to TBP/TATA-box.

Human and Drosophila TFIIA have three subunits: two large subunits, LN/alpha and LC/beta, derived from the same gene, and a small subunit, S/gamma. Yeast TFIIA has two subunits: a large TOA1 subunit that shows sequence similarity to the N-terminal of LN/alpha and the C-terminal of LC/beta, and a small subunit, TOA2 that is highly homologous with S/gamma. The conserved regions of the large and small subunits of TFIIA combine to form two domains: a four-helix bundle (helical domain) composed of two helices from each of the N-terminal regions of TOA1 and TOA2 in yeast; and a beta-barrel (beta-barrel domain) composed of beta-sheets from the C-terminal regions of TOA1 and TOA2 [PUBMED:8610010].

This entry represents the beta-barrel domain found at the C-terminal of the gamma subunit of transcription factor TFIIA.

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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Alignments

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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
(26)
Full
(357)
Representative proteomes NCBI
(301)
Meta
(1)
RP15
(74)
RP35
(115)
RP55
(178)
RP75
(214)
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Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(26)
Full
(357)
Representative proteomes NCBI
(301)
Meta
(1)
RP15
(74)
RP35
(115)
RP55
(178)
RP75
(214)
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
(26)
Full
(357)
Representative proteomes NCBI
(301)
Meta
(1)
RP15
(74)
RP35
(115)
RP55
(178)
RP75
(214)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

HMM logo

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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: Pfam-B_4941 (release 5.2)
Previous IDs: none
Type: Domain
Author: Bateman A, Mian N, Griffiths-Jones SR
Number in seed: 26
Number in full: 357
Average length of the domain: 50.30 aa
Average identity of full alignment: 52 %
Average coverage of the sequence by the domain: 42.76 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.2 21.2
Trusted cut-off 22.7 21.5
Noise cut-off 21.0 20.4
Model length: 52
Family (HMM) version: 9
Download: download the raw HMM for this family

Species distribution

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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 TFIIA_gamma_C domain has been found. There are 4 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 seqence.

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