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88  structures 1784  species 0  interactions 11025  sequences 94  architectures

Family: TFIIB (PF00382)

Summary: Transcription factor TFIIB repeat

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Transcription factor TFIIB repeat Provide feedback

No Pfam abstract.

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR013150

In eukaryotes, transcription initiation of all protein encoding genes involves the polymerase II system. This sytem is modulated by both general and specific transcription factors. The general factors (which include TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIG and TFIIH) operate through common promoter elements, such as the TATA box. Transcription factor IIB (TFIIB) is of central importance in transcription of class II genes. It associates with TFIID-TFIIA bound to DNA (the DA complex) to form a ternary TFIID-IIA-IBB (DAB) complex, which is recognised by RNA polymerase II [ PUBMED:1876184 , PUBMED:1949150 ]. TFIIB comprises ~315-340 residues and contains an imperfect C-terminal repeat of a 75-residue domain that may contribute to the symmetry of the folded protein. The basal archaeal transcription machinery resembles that of the eukaryotic polymerase II system and includes a homologue of TFIIB [ PUBMED:7597027 ].

This entry represents a cyclin-like domain which is found repeated in the C-terminal region of a variety of eukaryotic TFIIB's and their archaeal counterparts. These domains individually form the typical cyclin fold, and in the transcription complex they straddle the C-terminal region of the TATA-binding protein - an interaction essential for the formation of the transcription initiation complex [ PUBMED:9177165 , PUBMED:10619841 ].

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 Cyclin (CL0065), which has the following description:

This Clan contains cyclins, Transcription factor IIB (TFIIB), and the Retinoblastoma tumour suppressor proteins. These were predicted to be related by sequence [1].

The clan contains the following 12 members:

CDK5_activator Cyclin Cyclin_C Cyclin_C_2 Cyclin_N DUF3452 Herp-Cyclin K-cyclin_vir_C RB_A RB_B TFIIB TFIIB_C_1

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...

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.

  Seed
(13)
Full
(11025)
Representative proteomes UniProt
(28705)
RP15
(1948)
RP35
(5188)
RP55
(9357)
RP75
(13753)
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

  Seed
(13)
Full
(11025)
Representative proteomes UniProt
(28705)
RP15
(1948)
RP35
(5188)
RP55
(9357)
RP75
(13753)
Alignment:
Format:
Order:
Sequence:
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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.

  Seed
(13)
Full
(11025)
Representative proteomes UniProt
(28705)
RP15
(1948)
RP35
(5188)
RP55
(9357)
RP75
(13753)
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: Prosite
Previous IDs: transcript_fac2;
Type: Domain
Sequence Ontology: SO:0000417
Author: Finn RD
Number in seed: 13
Number in full: 11025
Average length of the domain: 90.60 aa
Average identity of full alignment: 24 %
Average coverage of the sequence by the domain: 38.60 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 23.6 23.6
Trusted cut-off 23.6 23.6
Noise cut-off 23.5 23.5
Model length: 92
Family (HMM) version: 21
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
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 TFIIB domain has been found. There are 88 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
A0A0P0X6J4 View 3D Structure Click here
A0A0P0X6J4 View 3D Structure Click here
A0A0R0JYX3 View 3D Structure Click here
A0A0R0JYX3 View 3D Structure Click here
A0A0R4IRB5 View 3D Structure Click here
A0A0R4IRB5 View 3D Structure Click here
A0A131MCT5 View 3D Structure Click here
A0A131MCT5 View 3D Structure Click here
A0A144A465 View 3D Structure Click here
A0A144A465 View 3D Structure Click here
A0A1D6ESJ9 View 3D Structure Click here
A0A1D6ETX0 View 3D Structure Click here
A0A1D6ETX0 View 3D Structure Click here
A0A1D6FJC6 View 3D Structure Click here
A0A1D6FJC6 View 3D Structure Click here
A0A1D6I9Y0 View 3D Structure Click here
A0A1D6I9Y0 View 3D Structure Click here
A0A1D6MBH4 View 3D Structure Click here
A0A1D6MBH4 View 3D Structure Click here
A0A1D6MBN6 View 3D Structure Click here
A0A1D6MBN6 View 3D Structure Click here
A0A1D6PIC7 View 3D Structure Click here
A0A1D6PIC7 View 3D Structure Click here
A0A1D8PT00 View 3D Structure Click here
A0A1D8PT00 View 3D Structure Click here
A4I187 View 3D Structure Click here
A4I187 View 3D Structure Click here
C4J4Z3 View 3D Structure Click here
C4J4Z3 View 3D Structure Click here
D4A8W8 View 3D Structure Click here
F1R9S3 View 3D Structure Click here
F1R9S3 View 3D Structure Click here
F4I4V4 View 3D Structure Click here
F4IN86 View 3D Structure Click here
F4IN86 View 3D Structure Click here
F4IW19 View 3D Structure Click here
F4IW19 View 3D Structure Click here
I1J8V2 View 3D Structure Click here
I1J8V2 View 3D Structure Click here
I1JG98 View 3D Structure Click here
I1JG98 View 3D Structure Click here
I1JNB0 View 3D Structure Click here
I1JNB0 View 3D Structure Click here
I1LHQ6 View 3D Structure Click here
I1LHQ6 View 3D Structure Click here
I1N8Y6 View 3D Structure Click here
I1N8Y6 View 3D Structure Click here
K7KNC5 View 3D Structure Click here
K7KNC5 View 3D Structure Click here
K7MF17 View 3D Structure Click here
K7MF17 View 3D Structure Click here
K7MXY1 View 3D Structure Click here
K7MXY1 View 3D Structure Click here
O13749 View 3D Structure Click here
O13749 View 3D Structure Click here
O16991 View 3D Structure Click here
O16991 View 3D Structure Click here
O23215 View 3D Structure Click here
O23215 View 3D Structure Click here
O82494 View 3D Structure Click here
P29052 View 3D Structure Click here
P29052 View 3D Structure Click here
P29055 View 3D Structure Click here
P29055 View 3D Structure Click here
P29056 View 3D Structure Click here
P29056 View 3D Structure Click here
P43072 View 3D Structure Click here
P43072 View 3D Structure Click here
P48512 View 3D Structure Click here
P48512 View 3D Structure Click here
P48513 View 3D Structure Click here
P48513 View 3D Structure Click here
P62915 View 3D Structure Click here
P62915 View 3D Structure Click here
P62916 View 3D Structure Click here
P62916 View 3D Structure Click here
Q00403 View 3D Structure Click here
Q00403 View 3D Structure Click here
Q0DJB2 View 3D Structure Click here
Q0DJB2 View 3D Structure Click here
Q0DUA7 View 3D Structure Click here
Q0WVQ3 View 3D Structure Click here
Q0WVQ3 View 3D Structure Click here
Q1PEE4 View 3D Structure Click here
Q1PEE4 View 3D Structure Click here
Q4E1P0 View 3D Structure Click here
Q4E1P0 View 3D Structure Click here
Q54FD6 View 3D Structure Click here
Q54FD6 View 3D Structure Click here
Q54U85 View 3D Structure Click here
Q54U85 View 3D Structure Click here
Q58192 View 3D Structure Click here
Q58192 View 3D Structure Click here
Q5AHZ3 View 3D Structure Click here
Q5AHZ3 View 3D Structure Click here
Q5KQD1 View 3D Structure Click here
Q5KQD1 View 3D Structure Click here
Q5TZ89 View 3D Structure Click here
Q5TZ89 View 3D Structure Click here
Q6Z467 View 3D Structure Click here
Q8CFK2 View 3D Structure Click here
Q8CFK2 View 3D Structure Click here
Q8H7W1 View 3D Structure Click here
Q8H7W1 View 3D Structure Click here
Q8I237 View 3D Structure Click here
Q8W0W3 View 3D Structure Click here
Q8W0W3 View 3D Structure Click here
Q92994 View 3D Structure Click here
Q92994 View 3D Structure Click here
Q9LIA6 View 3D Structure Click here
Q9LIA6 View 3D Structure Click here
Q9P6R0 View 3D Structure Click here
Q9P6R0 View 3D Structure Click here
Q9SS44 View 3D Structure Click here
Q9SS44 View 3D Structure Click here
Q9VEL2 View 3D Structure Click here
Q9VEL2 View 3D Structure Click here