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35  structures 1397  species 0  interactions 3945  sequences 64  architectures

Family: SNF5 (PF04855)

Summary: SNF5 / SMARCB1 / INI1

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.

SNF5 / SMARCB1 / INI1 Provide feedback

SNF5 is a component of the yeast SWI/SNF complex, which is an ATP-dependent nucleosome-remodelling complex that regulates the transcription of a subset of yeast genes. SNF5 is a key component of all SWI/SNF-class complexes characterised so far [1]. This family consists of the conserved region of SNF5, including a direct repeat motif. SNF5 is essential for the assembly promoter targeting and chromatin remodelling activity of the SWI-SNF complex [2]. SNF5 is also known as SMARCB1, for SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily b, member 1, and also INI1 for integrase interactor 1. Loss-of function mutations in SNF5 are thought to contribute to oncogenesis in malignant rhabdoid tumours (MRTs) [3].

Literature references

  1. Brzeski J, Podstolski W, Olczak K, Jerzmanowski A; , Nucleic Acids Res 1999;27:2393-2399.: Identification and analysis of the Arabidopsis thaliana BSH gene, a member of the SNF5 gene family. PUBMED:10325430 EPMC:10325430

  2. Geng F, Cao Y, Laurent BC; , Mol Cell Biol 2001;21:4311-4320.: Essential roles of Snf5p in Snf-Swi chromatin remodeling in vivo. PUBMED:11390659 EPMC:11390659

  3. Versteege I, Sevenet N, Lange J, Rousseau-Merck MF, Ambros P, Handgretinger R, Aurias A, Delattre O; , Nature 1998;394:203-206.: Truncating mutations of hSNF5/INI1 in aggressive paediatric cancer. PUBMED:9671307 EPMC:9671307


This tab holds annotation information from the InterPro database.

InterPro entry IPR006939

SNF5 is a component of the yeast SWI/SNF complex, which is an ATP-dependent nucleosome-remodelling complex that regulates the transcription of a subset of yeast genes. SNF5 is a key component of all SWI/SNF-class complexes characterised so far [ PUBMED:10325430 ]. This family consists of the conserved region of SNF5, including a direct repeat motif. SNF5 is essential for the assembly promoter targeting and chromatin remodelling activity of the SWI-SNF complex [ PUBMED:11390659 ]. SNF5 is also known as SMARCB1, for SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily b, member 1, and also INI1 for integrase interactor 1. Loss-of function mutations in SNF5 are thought to contribute to oncogenesis in malignant rhabdoid tumours (MRTs) [ PUBMED:9671307 ].

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...

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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
(92)
Full
(3945)
Representative proteomes UniProt
(6211)
RP15
(713)
RP35
(1700)
RP55
(2959)
RP75
(4014)
Jalview 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
(92)
Full
(3945)
Representative proteomes UniProt
(6211)
RP15
(713)
RP35
(1700)
RP55
(2959)
RP75
(4014)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(92)
Full
(3945)
Representative proteomes UniProt
(6211)
RP15
(713)
RP35
(1700)
RP55
(2959)
RP75
(4014)
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: Pfam-B_6054 (release 7.6)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Kerrison ND
Number in seed: 92
Number in full: 3945
Average length of the domain: 163.1 aa
Average identity of full alignment: 29 %
Average coverage of the sequence by the domain: 41.25 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.8 21.8
Trusted cut-off 22.1 21.8
Noise cut-off 21.6 21.7
Model length: 236
Family (HMM) version: 15
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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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...

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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 SNF5 domain has been found. There are 35 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
A0A044V447 View 3D Structure Click here
A0A077Z865 View 3D Structure Click here
A0A077ZGX7 View 3D Structure Click here
A0A0D2DQN1 View 3D Structure Click here
A0A0D2GTU8 View 3D Structure Click here
A0A0K0EFH3 View 3D Structure Click here
A0A158Q6L2 View 3D Structure Click here
A0A175W9L6 View 3D Structure Click here
A0A1C1CCQ0 View 3D Structure Click here
A0A1C1D3D5 View 3D Structure Click here
A0A1D6FUW7 View 3D Structure Click here
A0A1D8PEB6 View 3D Structure Click here
A0A1D8PJZ6 View 3D Structure Click here
A0A2R8QP61 View 3D Structure Click here
A0A3P7E2B8 View 3D Structure Click here
A0A3Q0KG84 View 3D Structure Click here
C0NIG8 View 3D Structure Click here
C0NWB2 View 3D Structure Click here
C1H731 View 3D Structure Click here
C1H9M8 View 3D Structure Click here
D7RJ53 View 3D Structure Click here
K7MJX2 View 3D Structure Click here
P18480 View 3D Structure Click here
P93045 View 3D Structure Click here
Q06168 View 3D Structure Click here
Q09699 View 3D Structure Click here
Q0DY00 View 3D Structure Click here
Q12824 View 3D Structure Click here
Q21831 View 3D Structure Click here
Q24090 View 3D Structure Click here
Q4KLI0 View 3D Structure Click here
Q54WV6 View 3D Structure Click here
Q5BIN2 View 3D Structure Click here
Q5U379 View 3D Structure Click here
Q5ZK40 View 3D Structure Click here
Q6C9N2 View 3D Structure Click here
Q6CSR7 View 3D Structure Click here
Q6DFM1 View 3D Structure Click here
Q6FTV3 View 3D Structure Click here
Q754R8 View 3D Structure Click here