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62  structures 377  species 2  interactions 4036  sequences 51  architectures

Family: SNARE (PF05739)

Summary: SNARE domain

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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.

SNARE domain Provide feedback

Most if not all vesicular membrane fusion events in eukaryotic cells are believed to be mediated by a conserved fusion machinery, the SNARE [soluble N-ethylmaleimide-sensitive factor (NSF) attachment protein (SNAP) receptors] machinery. The SNARE domain is thought to act as a protein-protein interaction module in the assembly of a SNARE protein complex [1].

Literature references

  1. Weimbs T, Low SH, Chapin SJ, Mostov KE, Bucher P, Hofmann K; , Proc Natl Acad Sci U S A 1997;94:3046-3051.: A conserved domain is present in different families of vesicular fusion proteins: a new superfamily. PUBMED:9096343 EPMC:9096343


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000727

The process of vesicular fusion with target membranes depends on a set of SNAREs (SNAP-Receptors), which are associated with the fusing membranes [PUBMED:9239749, PUBMED:9232812]. Target SNAREs (t-SNAREs) are localised on the target membrane and belong to two different families, the syntaxin-like family and the SNAP-25 like family. One member of each family, together with a v-SNARE localised on the vesicular membrane, are required for fusion.

The Syntaxins are type-I transmembrane proteins that contain several regions with coiled-coil propensity in their cytosolic part, the SNARE motif. SNAP-25 (INTERPRO) is a protein consisting of two coiled-coil regions, which is associated with the membrane by lipid anchors. SNARE motifs assemble into parallel four helix bundles stabilised by the burial of these hydrophobic helix faces in the bundle core. Monomeric SNARE motifs are disordered so this assembly reaction is accompanied by a dramatic increase in alpha-helical secondary structure [PUBMED:14570579]. The parallel arrangement of SNARE motifs within complexes bring the transmembrane anchors, and the two membranes, into close proximity. Recently, it was shown that the two coiled-coil regions of SNAP-25 and one of the coiled-coil regions of the syntaxins are related [PUBMED:9096343]. This domain is found in both Syntaxin and SNAP-25 families as well as in other proteins.

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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Pfam Clan

This family is a member of clan SNARE-fusion (CL0445), which contains the following 4 members:

SNARE Synaptobrevin Syntaxin Syntaxin_2

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...

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
(105)
Full
(4036)
Representative proteomes NCBI
(3820)
Meta
(24)
RP15
(824)
RP35
(1372)
RP55
(2046)
RP75
(2609)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(105)
Full
(4036)
Representative proteomes NCBI
(3820)
Meta
(24)
RP15
(824)
RP35
(1372)
RP55
(2046)
RP75
(2609)
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
(105)
Full
(4036)
Representative proteomes NCBI
(3820)
Meta
(24)
RP15
(824)
RP35
(1372)
RP55
(2046)
RP75
(2609)
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.

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.

Pfam alignments:

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_6285 (release 8.0)
Previous IDs: none
Type: Family
Author: Moxon SJ
Number in seed: 105
Number in full: 4036
Average length of the domain: 61.80 aa
Average identity of full alignment: 22 %
Average coverage of the sequence by the domain: 22.43 %

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 30.0 30.0
Trusted cut-off 30.0 30.0
Noise cut-off 29.9 29.9
Model length: 63
Family (HMM) version: 14
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 2 interactions for this family. More...

Synaptobrevin SNARE

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 SNARE domain has been found. There are 62 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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