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0  structures 54  species 0  interactions 472  sequences 17  architectures

Family: HMG14_17 (PF01101)

Summary: HMG14 and HMG17

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This is the Wikipedia entry entitled "High mobility group protein HMG14 and HMG17". More...

High mobility group protein HMG14 and HMG17 Edit Wikipedia article

HMG14 and HMG17
Identifiers
Symbol HMG14_17
Pfam PF01101
InterPro IPR000079
PROSITE PDOC00307

High mobility group protein HMG14 and HMG17 also known as nucleosomal binding domain is a family of evolutionarily related proteins.

High mobility group (HMG) proteins constitute a family of relatively low molecular weight non-histone components in chromatin. HMG14 and HMG17 are highly-similar proteins of about 100 amino acid residues; the sequence of chicken HMG14 is almost as similar to chicken HMG17 as it is to mammalian HMG14 polypeptides.[1] The proteins bind to the inner side of the nucleosomal DNA, altering the interaction between the DNA and the histone octamer. It is thought that they may be involved in the process that confers specific chromatin conformations to transcribable regions in the genome.[2]

The SMART signature describes a nucleosomal binding domain, which facilitates binding of proteins to nucleosomes in chromatin. The domain is most commonly found in the high mobility group (HMG) proteins, HMG14 and HMG17, however, it is also found in other proteins which bind to nucleosomes, e.g. NBP-45. NBP-45 is a nucleosomal binding protein, first identified in mice,[3] which is related to HMG14 and HMG17. NBP-45 binds specifically to nucleosome core particles, and can function as a transcriptional activator. These findings led to the suggestion that this domain, common to NBP-45, HMG14 and HMG17 is responsible for binding of the proteins to nucleosomes in chromatin.

Examples

Human proteins containing this domain include:

References

  1. ^ Dodgson JB, Browne DL, Black AJ (1988). "Chicken chromosomal protein HMG-14 and HMG-17 cDNA clones: isolation, characterization and sequence comparison". Gene 63 (2): 287–295. doi:10.1016/0378-1119(88)90532-X. PMID 3384337. 
  2. ^ Gonzalez FJ, Bustin M, Landsman D, Soares N (1986). "Chromosomal protein HMG-17. Complete human cDNA sequence and evidence for a multigene family". J. Biol. Chem. 261 (16): 7479–7484. PMID 3754870. 
  3. ^ Bustin M, Landsman D, Shirakawa H, Postnikov YV (2000). "NBP-45, a novel nucleosomal binding protein with a tissue-specific and developmentally regulated expression". J. Biol. Chem. 275 (9): 6368–6374. doi:10.1074/jbc.275.9.6368. PMID 10692437. 

This article incorporates text from the public domain Pfam and InterPro IPR000079

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000079

This entry represents the HMGN family, whose members promote chromatin unfolding, enhance access to nucleosomes, and modulate transcription from chromatin templates. HMGNs are expressed only in vertebrates [PUBMED:25281808].

The high mobility group (HMG) proteins are the most abundant and ubiquitous nonhistone chromosomal proteins. They bind to DNA and to nucleosomes and are involved in the regulation of DNA-dependent processes such as transcription, replication, recombination, and DNA repair. They can be grouped into three families: HMGB (HMG 1/2), HMGN (HMG 14/17) and HMGA (HMG I/Y). The characteristic domains are: AT-hook for the HMGA family, the HMG Box for the HMGB family, and the nucleosome-binding domain (NBD) for the members of the HMGN family [PUBMED:25281808].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

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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.

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RP35
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RP55
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RP75
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  Seed
(75)
Full
(472)
Representative proteomes UniProt
(845)
NCBI
(1475)
Meta
(0)
RP15
(38)
RP35
(136)
RP55
(235)
RP75
(408)
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
(75)
Full
(472)
Representative proteomes UniProt
(845)
NCBI
(1475)
Meta
(0)
RP15
(38)
RP35
(136)
RP55
(235)
RP75
(408)
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.

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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.

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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: Prosite
Previous IDs: none
Type: Family
Author: Finn RD, Bateman A
Number in seed: 75
Number in full: 472
Average length of the domain: 88.90 aa
Average identity of full alignment: 50 %
Average coverage of the sequence by the domain: 68.10 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 11927849 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 23.5 23.5
Trusted cut-off 24.3 24.0
Noise cut-off 21.9 21.9
Model length: 91
Family (HMM) version: 15
Download: download the raw HMM for this family

Species distribution

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