Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
0  structures 24  species 0  interactions 24  sequences 1  architecture

Family: SWC7 (PF17330)

Summary: SWR1 chromatin-remodelling complex, subunit Swc7

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

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.

SWR1 chromatin-remodelling complex, subunit Swc7 Provide feedback

Th SWR1 complex is involved in chromatin-remodelling by promoting the the ATP-dependent exchange of histone H2A for the H2A variant HZT1 in Saccharomyces cerevisiae or H2AZ in mammals. The SWR1 chromatin-remodelling complex is composed of at least 14 subunits and has a molecular mass of about 1.2 to 1.5 MDa. In S. cerevisiae there are core conserved subunits (ATPase; Swr1,RuvB-like; Rvb1 and Rvb2, Actin; Act1, Actin-related: Arp4 and Arp6, YEATS protein; [1]) and non-conserved subunits ( Vps71 (Swc6), Vps72 (Swc2), Swc3, Swc4, Swc5, Swc7, Bdf1 [2]). Seven of the SWR1 subunits are involved in maintaining complex integrity and H2AZ histone replacement activity: Swr1, Swc2, Swc3, Arp6, Swc5, Yaf9 and Swc6. Arp4 is required for the association of Bdf1, Yaf9, and Swc4 and Arp4 is also required for SWR1 H2AZ histone replacement activity in vitro. Furthermore the N-terminal region of the ATPase Swr1 provides the platform upon which Bdf1, Swc7, Arp4, Act1, Yaf9 and Swc4 associate [3]. It also contains an additional H2AZ-H2B specific binding site, distinct from the binding site of the Swc2 subunit [4]. In eukaryotes the deposition of variant histones into nucleosomes by the chromatin-remodelling complexes such as the SWR1 and INO80 complexes have many crucial functions including the control of gene regulation and expression, checkpoint regulation, DNA replication and repair, telomer maintenance and chromosomal segregation and as such represent critical components of pathways that maintain genomic integrity. This entry represents the subunit Swc7; the smallest subunit of the SWR1 complex. Swc7 is not required for H2AZ binding. It associates with the N terminus of Swr1, and the association of Bdf1 requires Swc7, Yaf9, and Arp4 [3].

Literature references

  1. Schulze JM, Wang AY, Kobor MS;, Biochem Cell Biol. 2009;87:65-75.: YEATS domain proteins: a diverse family with many links to chromatin modification and transcription. PUBMED:19234524 EPMC:19234524

  2. Morrison AJ, Shen X;, Nat Rev Mol Cell Biol. 2009;10:373-384.: Chromatin remodelling beyond transcription: the INO80 and SWR1 complexes. PUBMED:19424290 EPMC:19424290

  3. Morrison AJ, Shen X;, Nat Rev Mol Cell Biol. 2009;10:373-384.: Chromatin remodelling beyond transcription: the INO80 and SWR1 complexes. PUBMED:19424290 EPMC:19424290

  4. Morrison AJ, Shen X;, Nat Rev Mol Cell Biol. 2009;10:373-384.: Chromatin remodelling beyond transcription: the INO80 and SWR1 complexes. PUBMED:19424290 EPMC:19424290


This tab holds annotation information from the InterPro database.

No InterPro data for this Pfam family.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

Loading domain graphics...

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, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics 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
(16)
Full
(24)
Representative proteomes UniProt
(42)
NCBI
(48)
Meta
(0)
RP15
(1)
RP35
(8)
RP55
(14)
RP75
(23)
Jalview View  View  View  View  View  View  View  View   
HTML View  View               
PP/heatmap 1 View               

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(16)
Full
(24)
Representative proteomes UniProt
(42)
NCBI
(48)
Meta
(0)
RP15
(1)
RP35
(8)
RP55
(14)
RP75
(23)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

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
(16)
Full
(24)
Representative proteomes UniProt
(42)
NCBI
(48)
Meta
(0)
RP15
(1)
RP35
(8)
RP55
(14)
RP75
(23)
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.

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

This family is new in this Pfam release.

Seed source: PRODOM:PD072365
Previous IDs: none
Type: Family
Author: El-Gebali S
Number in seed: 16
Number in full: 24
Average length of the domain: 100.30 aa
Average identity of full alignment: 46 %
Average coverage of the sequence by the domain: 77.30 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.0 25.0
Trusted cut-off 109.0 99.3
Noise cut-off 22.8 22.1
Model length: 98
Family (HMM) version: 1
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Hide

Weight segments by...


Change the size of the sunburst

Small
Large

Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

Align selected sequences to HMM

Generate a FASTA-format file

Clear selection

This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

Loading sunburst data...

Tree controls

Hide

The tree shows the occurrence of this domain across different species. More...

Loading...

Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.