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4  structures 147  species 0  interactions 456  sequences 5  architectures

Family: Basic (PF01586)

Summary: Myogenic Basic domain

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This is the Wikipedia entry entitled "Myogenic determination factor 5". More...

Myogenic determination factor 5 Edit Wikipedia article

Myf5 domain
Identifiers
Symbol Myf5
Pfam PF12232
InterPro IPR022032
Basic domain
PDB 1mdy EBI.jpg
crystal structure of myod bhlh domain bound to dna: perspectives on dna recognition and implications for transcriptional activation
Identifiers
Symbol Basic
Pfam PF01586
InterPro IPR002546
PROSITE PDOC00038
SCOP 1mdy
SUPERFAMILY 1mdy

In molecular biology, the myogenic determination factor 5 proteins are a family of proteins found in eukaryotes. This family includes the Myf5 protein, which is responsible for directing cells to the skeletal myocyte lineage during development. Myf5 is likely to act in a similar way to the other MRF4 proteins such as MyoD which perform the same function. These are histone acetyltransferases and histone deacetylases which activate and repress genes involved in the myocyte lineage.

Myogenic determination factor 5 proteins contain three conserved protein domains. A C-terminal Myf5 domain, a central basic helix-loop-helix (bHLH) domain and an N-terminal basic domain. The bHLH region mediates specific DNA binding.[1] With 12 residues of the basic domain involved in DNA binding.[2] The basic domain forms an extended alpha helix in the structure.

References[edit]

  1. ^ Hamamori Y, Wu HY, Sartorelli V, Kedes L (November 1997). "The basic domain of myogenic basic helix-loop-helix (bHLH) proteins is the novel target for direct inhibition by another bHLH protein, Twist". Mol. Cell. Biol. 17 (11): 6563–73. PMC 232510. PMID 9343420. 
  2. ^ Molkentin JD, Olson EN (September 1996). "Combinatorial control of muscle development by basic helix-loop-helix and MADS-box transcription factors". Proc. Natl. Acad. Sci. U.S.A. 93 (18): 9366–73. doi:10.1073/pnas.93.18.9366. PMC 38433. PMID 8790335. 

This article incorporates text from the public domain Pfam and InterPro IPR022032

This article incorporates text from the public domain Pfam and InterPro IPR002546

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.

Myogenic Basic domain Provide feedback

This basic domain is found in the MyoD family of muscle specific proteins that control muscle development. The bHLH region of the MyoD family includes the basic domain and the Helix-loop-helix (HLH) motif. The bHLH region mediates specific DNA binding [1]. With 12 residues of the basic domain involved in DNA binding [2]. The basic domain forms an extended alpha helix in the structure.

Literature references

  1. Hamamori Y, Wu HY, Sartorelli V, Kedes L; , Mol Cell Biol 1997;17:6563-6573.: The basic domain of myogenic basic helix-loop-helix (bHLH) proteins is the novel target for direct inhibition by another bHLH protein, Twist. PUBMED:9343420 EPMC:9343420

  2. Molkentin JD, Olson EN; , Proc Natl Acad Sci U S A 1996;93:9366-9373.: Combinatorial control of muscle development by basic helix-loop-helix and MADS-box transcription factors. PUBMED:8790335 EPMC:8790335


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002546

This basic domain is found in the MyoD family of muscle specific proteins that control muscle development. The bHLH region of the MyoD family includes the basic domain and the Helix-loop-helix (HLH) motif. The bHLH region mediates specific DNA binding [PUBMED:9343420]. With 12 residues of the basic domain involved in DNA binding [PUBMED:8790335]. The basic domain forms an extended alpha helix in the structure.

Gene Ontology

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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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics 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.

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(7)
Full
(456)
Representative proteomes NCBI
(408)
Meta
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RP15
(21)
RP35
(30)
RP55
(72)
RP75
(145)
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Format an alignment

  Seed
(7)
Full
(456)
Representative proteomes NCBI
(408)
Meta
(0)
RP15
(21)
RP35
(30)
RP55
(72)
RP75
(145)
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
(7)
Full
(456)
Representative proteomes NCBI
(408)
Meta
(0)
RP15
(21)
RP35
(30)
RP55
(72)
RP75
(145)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download    
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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.

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.

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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_427 (release 4.1)
Previous IDs: none
Type: Family
Author: Bashton M, Bateman A
Number in seed: 7
Number in full: 456
Average length of the domain: 84.90 aa
Average identity of full alignment: 40 %
Average coverage of the sequence by the domain: 34.53 %

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 25.0 25.0
Trusted cut-off 27.1 26.1
Noise cut-off 20.9 20.9
Model length: 86
Family (HMM) version: 11
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 Basic 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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