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0  structures 953  species 0  interactions 2819  sequences 193  architectures

Family: WSD (PF15613)

Summary: Williams-Beuren syndrome DDT (WSD), D-TOX E motif

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Williams-Beuren syndrome DDT (WSD), D-TOX E motif Provide feedback

This family represents the combined alpha-helical module found in diverse eukaryotic chromatin proteins [1]. Based on the Ioc3 structure, the N-terminus of this module is inferred to interact with nucleosomal linker DNA and the SLIDE domain of ISWI proteins [1,2]. The resulting complex forms a protein ruler that measures out the spacing between two adjacent nucleosomes [2]. The acidic residue from the GxD signature at the N-terminus is a major determinant of the interaction between the ISWI and WHIM motifs. The N-terminal portion also contacts the inter-nucleosomal linker DNA. The module shows a great domain architectural diversity and is often combined with other modified histone peptide recognizing and DNA binding domains, some of which discriminate methylated DNA. The WSD module constitutes the inter-nucleosomal linker DNA binding site in the major groove of DNA [1] and was first identified as WSD [3] the D-TOX E motif of plant homeodomains homologous with the mutant transcription factor causing Williams-Beuren syndrome in association with the DDT-domain.

Literature references

  1. Aravind L, Iyer LM;, Cell Cycle. 2012;11:119-131.: The HARE-HTH and associated domains: novel modules in the coordination of epigenetic DNA and protein modifications. PUBMED:22186017 EPMC:22186017

  2. Yamada K, Frouws TD, Angst B, Fitzgerald DJ, DeLuca C, Schimmele K, Sargent DF, Richmond TJ;, Nature. 2011;472:448-453.: Structure and mechanism of the chromatin remodelling factor ISW1a. PUBMED:21525927 EPMC:21525927

  3. Mukherjee K, Brocchieri L, Burglin TR;, Mol Biol Evol. 2009;26:2775-2794.: A comprehensive classification and evolutionary analysis of plant homeobox genes. PUBMED:19734295 EPMC:19734295


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR028941

This entry represents the WHIM2 domain found in diverse eukaryotic chromatin proteins, such as animal BAZ/WAL and BPTF proteins, plant RLT and MBD9, and yeast Itc1. This domain contains the D-TOX E motif (also known as the Williams-Beuren syndrome DDT (WSD) motif) that is conserved from yeasts to animals [PUBMED:22186017, PUBMED:21525927, PUBMED:19734295].

WHIM2 domain is a conserved alpha helical motif that along with the WHIM1 and WHIM3 motifs, and the DDT domain comprise an alpha helical module found in diverse eukaryotic chromatin proteins [PUBMED:22186017]. Based on the Ioc3 structure, this module is inferred to interact with nucleosomal linker DNA and the SLIDE domain of ISWI proteins [PUBMED:22186017, PUBMED:21525927]. The resulting complex forms a protein ruler that measures out the spacing between two adjacent nucleosomes [PUBMED:21525927]. The acidic residue from the GxD signature of WHIM2 is a major determinant of the interaction between the ISWI and WHIM motifs. The N-terminal portion of the WHIM2 motif also contacts the inter-nucleosomal linker DNA. The module shows a great domain architectural diversity and is often combined with other modified histone peptide recognizing and DNA binding domains, some of which discriminate methylated DNA [PUBMED:22186017].

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.

  Seed
(82)
Full
(2819)
Representative proteomes UniProt
(4053)
NCBI
(9048)
Meta
(2)
RP15
(596)
RP35
(1259)
RP55
(1917)
RP75
(2247)
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  Seed
(82)
Full
(2819)
Representative proteomes UniProt
(4053)
NCBI
(9048)
Meta
(2)
RP15
(596)
RP35
(1259)
RP55
(1917)
RP75
(2247)
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
(82)
Full
(2819)
Representative proteomes UniProt
(4053)
NCBI
(9048)
Meta
(2)
RP15
(596)
RP35
(1259)
RP55
(1917)
RP75
(2247)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

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: Manual
Previous IDs: WHIM2;
Type: Family
Sequence Ontology: SO:0100021
Author: Iyer LM , Aravind L , Burglin T
Number in seed: 82
Number in full: 2819
Average length of the domain: 104.60 aa
Average identity of full alignment: 25 %
Average coverage of the sequence by the domain: 7.28 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.4 25.4
Trusted cut-off 25.4 25.4
Noise cut-off 25.3 25.3
Model length: 99
Family (HMM) version: 6
Download: download the raw HMM for this family

Species distribution

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