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64  structures 1363  species 0  interactions 18783  sequences 190  architectures

Family: SRF-TF (PF00319)

Summary: SRF-type transcription factor (DNA-binding and dimerisation domain)

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SRF-type transcription factor (DNA-binding and dimerisation domain) Provide feedback

No Pfam abstract.

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002100

Human serum response factor (SRF) is a ubiquitous nuclear protein important for cell proliferation and differentiation. SRF function is essential for transcriptional regulation of numerous growth-factor-inducible genes, such as c-fos oncogene and muscle-specific actin genes. A core domain of around 90 amino acids is sufficient for the activities of DNA-binding, dimerisation and interaction with accessory factors. Within the core is a DNA-binding region, designated the MADS box [ PUBMED:7637780 ], that is highly similar to many eukaryotic regulatory proteins: among these are MCM1, the regulator of cell type-specific genes in fission yeast; DSRF, a Drosophila trachea development factor; the MEF2 family of myocyte-specific enhancer factors; and the Agamous and Deficiens families of plant homeotic proteins.

In SRF, the MADS box has been shown to be involved in DNA-binding and dimerisation [ PUBMED:3203386 ]. Proteins belonging to the MADS family function as dimers, the primary DNA-binding element of which is an anti-parallel coiled coil of two amphipathic alpha-helices, one from each subunit. The DNA wraps around the coiled coil allowing the basic N-termini of the helices to fit into the DNA major groove. The chain extending from the helix N-termini reaches over the DNA backbone and penetrates into the minor groove. A 4-stranded, anti-parallel beta-sheet packs against the coiled-coil face opposite the DNA and is the central element of the dimerisation interface. The MADS-box domain is commonly found associated with K-box region see ( INTERPRO ).

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

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
(231)
Full
(18783)
Representative proteomes UniProt
(34326)
RP15
(1847)
RP35
(8559)
RP55
(14975)
RP75
(20950)
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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
(231)
Full
(18783)
Representative proteomes UniProt
(34326)
RP15
(1847)
RP35
(8559)
RP55
(14975)
RP75
(20950)
Alignment:
Format:
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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
(231)
Full
(18783)
Representative proteomes UniProt
(34326)
RP15
(1847)
RP35
(8559)
RP55
(14975)
RP75
(20950)
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 & Pfam-B_6396 (Release 8.0)
Previous IDs: transcript_fact;
Type: Domain
Sequence Ontology: SO:0000417
Author: Finn RD
Number in seed: 231
Number in full: 18783
Average length of the domain: 47.10 aa
Average identity of full alignment: 49 %
Average coverage of the sequence by the domain: 16.91 %

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 20.4 20.4
Trusted cut-off 20.4 20.4
Noise cut-off 20.3 20.3
Model length: 48
Family (HMM) version: 20
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 SRF-TF domain has been found. There are 64 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
A0A060CXE4 View 3D Structure Click here
A0A060CXH0 View 3D Structure Click here
A0A060D0N9 View 3D Structure Click here
A0A060D145 View 3D Structure Click here
A0A060D762 View 3D Structure Click here
A0A060D937 View 3D Structure Click here
A0A096MJY4 View 3D Structure Click here
A0A0G2KPL1 View 3D Structure Click here
A0A0N7KCW7 View 3D Structure Click here
A0A0N7KIY8 View 3D Structure Click here
A0A0P0VBS2 View 3D Structure Click here
A0A0P0VC04 View 3D Structure Click here
A0A0P0VDS5 View 3D Structure Click here
A0A0P0W5T9 View 3D Structure Click here
A0A0P0WS55 View 3D Structure Click here
A0A0P0WWA7 View 3D Structure Click here
A0A0P0XHJ8 View 3D Structure Click here
A0A0P0XI85 View 3D Structure Click here
A0A0P0XN39 View 3D Structure Click here
A0A0P0Y4X8 View 3D Structure Click here
A0A0R0E723 View 3D Structure Click here
A0A0R0E743 View 3D Structure Click here
A0A0R0EAX1 View 3D Structure Click here
A0A0R0EIM6 View 3D Structure Click here
A0A0R0EV26 View 3D Structure Click here
A0A0R0EWG4 View 3D Structure Click here
A0A0R0EWH8 View 3D Structure Click here
A0A0R0EX62 View 3D Structure Click here
A0A0R0FC28 View 3D Structure Click here
A0A0R0G677 View 3D Structure Click here
A0A0R0G8B9 View 3D Structure Click here
A0A0R0GU09 View 3D Structure Click here
A0A0R0H9T9 View 3D Structure Click here
A0A0R0HJ53 View 3D Structure Click here
A0A0R0HQX6 View 3D Structure Click here
A0A0R0HQZ0 View 3D Structure Click here
A0A0R0HSP0 View 3D Structure Click here
A0A0R0HYT5 View 3D Structure Click here
A0A0R0HZ66 View 3D Structure Click here
A0A0R0HZB4 View 3D Structure Click here
A0A0R0I6S8 View 3D Structure Click here
A0A0R0II46 View 3D Structure Click here
A0A0R0IIX9 View 3D Structure Click here
A0A0R0ISX6 View 3D Structure Click here
A0A0R0IX28 View 3D Structure Click here
A0A0R0J4N4 View 3D Structure Click here
A0A0R0JCG7 View 3D Structure Click here
A0A0R0JCU0 View 3D Structure Click here
A0A0R0JPQ8 View 3D Structure Click here
A0A0R0JXK1 View 3D Structure Click here
A0A0R0KBY2 View 3D Structure Click here
A0A0R0KM60 View 3D Structure Click here
A0A0R0KVD4 View 3D Structure Click here
A0A0R0KYZ0 View 3D Structure Click here
A0A0R0L3Q0 View 3D Structure Click here
A0A0R0L5G2 View 3D Structure Click here
A0A0R0L878 View 3D Structure Click here
A0A0R0LDF2 View 3D Structure Click here
A0A0R4ITE5 View 3D Structure Click here
A0A140LGW3 View 3D Structure Click here
A0A1D6E786 View 3D Structure Click here
A0A1D6E941 View 3D Structure Click here
A0A1D6ESU4 View 3D Structure Click here
A0A1D6FAE8 View 3D Structure Click here
A0A1D6FGI5 View 3D Structure Click here
A0A1D6FPY5 View 3D Structure Click here
A0A1D6GGX0 View 3D Structure Click here
A0A1D6H1J3 View 3D Structure Click here
A0A1D6H9I5 View 3D Structure Click here
A0A1D6HG08 View 3D Structure Click here
A0A1D6HJ96 View 3D Structure Click here
A0A1D6HL27 View 3D Structure Click here
A0A1D6HQG7 View 3D Structure Click here
A0A1D6HRH9 View 3D Structure Click here
A0A1D6HRZ7 View 3D Structure Click here
A0A1D6HW69 View 3D Structure Click here
A0A1D6I275 View 3D Structure Click here
A0A1D6I854 View 3D Structure Click here
A0A1D6IJ33 View 3D Structure Click here
A0A1D6IV93 View 3D Structure Click here
A0A1D6JR01 View 3D Structure Click here
A0A1D6JT79 View 3D Structure Click here
A0A1D6KJS6 View 3D Structure Click here
A0A1D6KJW4 View 3D Structure Click here
A0A1D6KJX3 View 3D Structure Click here
A0A1D6KP78 View 3D Structure Click here
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A0A1D6L4V6 View 3D Structure Click here
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A0A1D6P230 View 3D Structure Click here
A0A1D6P8V7 View 3D Structure Click here
A0A1D6PGX4 View 3D Structure Click here
A0A1D6PNS1 View 3D Structure Click here
A0A1D6PX18 View 3D Structure Click here
A0A1D6Q3S4 View 3D Structure Click here
A0A1D6Q718 View 3D Structure Click here
A0A1D6QE35 View 3D Structure Click here
A0A1D8PL95 View 3D Structure Click here
A0A1P8ASZ9 View 3D Structure Click here
A0A1P8AT79 View 3D Structure Click here
A0A1P8B5J4 View 3D Structure Click here
A0A368UGH5 View 3D Structure Click here
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A1XG54 View 3D Structure Click here
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I1KY27 View 3D Structure Click here
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I1LN54 View 3D Structure Click here
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I1LS77 View 3D Structure Click here
I1LW12 View 3D Structure Click here
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K7LIB1 View 3D Structure Click here
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O04632 View 3D Structure Click here
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O81421 View 3D Structure Click here
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P07249 View 3D Structure Click here
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P38128 View 3D Structure Click here
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Q02078 View 3D Structure Click here
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Q06413 View 3D Structure Click here
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