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40  structures 380  species 1  interaction 2176  sequences 31  architectures

Family: Synaptobrevin (PF00957)

Summary: Synaptobrevin

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This is the Wikipedia entry entitled "Synaptobrevin". More...

Synaptobrevin Edit Wikipedia article

Synaptobrevin
Coresnarecomplex.png
Three different views of the high resolution structure of a truncated neuronal SNARE complex. Legend: synaptobrevin-2 (red), Syntaxin-1 (violet), SNAP-25 (purple).
Identifiers
Symbol Synaptobrevin
Pfam PF00957
InterPro IPR001388
PROSITE PDOC00368
SCOP 1sfc
SUPERFAMILY 1sfc
OPM superfamily 218
OPM protein 3dh7

Synaptobrevins (synaptobrevin isotypes 1-2) are small integral membrane proteins of secretory vesicles with molecular weight of 18 kilodalton (kDa) that are part of the vesicle-associated membrane protein (VAMP) family.[1][2][3][4][5]

Synaptobrevin is one of the SNARE proteins involved in formation of the SNARE complexes.

Structure

Out of four α-helices of the core SNARE complex one is contributed by synaptobrevin, one by syntaxin, and two by SNAP-25 (in neurons).

Function

SNARE proteins are the key components of the molecular machinery that drives fusion of membranes in exocytosis. Their function however is subject to fine-tuning by various regulatory proteins collectively referred to as SNARE masters.

Classification

In the Q/R nomenclature for organizing SNARE proteins, VAMP/synaptobrevin family members are classified as R-SNAREs, so named for the presence of an arginine at a specific location within the primary sequence of the protein (as opposed to the SNAREs of the target membrane, which contain a glutamine and are so named Q-SNAREs). Synaptobrevin is classified as a V-SNARE in the V/T nomenclature, an alternative classification scheme in which SNAREs are classified as V-SNAREs and T-SNAREs for their localization to vesicles and target membranes, respectively.[6]

Clinical significance

Synaptobrevin is degraded by tetanospasmin, a protein derived from the bacterium Clostridium tetani, which causes tetanus. A related bacterium, Clostridium botulinum, produces botulinum toxin that also hydrolyzes synaptobrevin.

Human proteins containing this domain

SEC22A; SEC22B; SYBL1; VAMP1; VAMP2; VAMP3; VAMP4; VAMP5; VAMP8; YKT6;

References and notes

  1. ^ Baumert M, Maycox PR, Navone F, De Camilli P, Jahn R (February 1, 1989). "Synaptobrevin: an integral membrane protein of 18,000 daltons present in small synaptic vesicles of rat brain". EMBO J 8 (2): 379–84. PMC 400817. PMID 2498078. 
  2. ^ Bock JB, Scheller RH (October 1999). "SNARE proteins mediate lipid bilayer fusion". Proc. Natl. Acad. Sci. U.S.A. 96 (22): 12227–9. doi:10.1073/pnas.96.22.12227. PMC 34255. PMID 10535902. 
  3. ^ Ernst JA, Brunger AT (2003). "High resolution structure, stability, and synaptotagmin binding of a truncated neuronal SNARE complex". J Biol Chem 278 (10): 8630–6. doi:10.1074/jbc.M211889200. PMID 12496247. 
  4. ^ Fasshauer D, Sutton RB, Brunger AT, Jahn R (December 1998). "Conserved structural features of the synaptic fusion complex: SNARE proteins reclassified as Q- and R-SNAREs". Proc. Natl. Acad. Sci. U.S.A. 95 (26): 15781–6. doi:10.1073/pnas.95.26.15781. PMC 28121. PMID 9861047. 
  5. ^ Weber T, Zemelman BV, McNew JA, Westermann B, Gmachl M, Parlati F, Sollner TH, Rothman JE (1998). "SNAREpins: minimal machinery for membrane fusion". Cell 92 (6): 759–72. doi:10.1016/S0092-8674(00)81404-X. PMID 9529252. 
  6. ^ Juan S. Bonifacino and Benjamin S. Glick. "The Mechanisms of Vesicle Budding and Fusion." Cell, Vol. 116, 153–166, January 23, 2004,

External links

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

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.

Synaptobrevin Provide feedback

No Pfam abstract.

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001388

Synaptobrevin is an intrinsic membrane protein of small synaptic vesicles [PUBMED:2560644], specialised secretory organelles of neurons that actively accumulate neurotransmitters and participate in their calcium-dependent release by exocytosis. Vesicle function is mediated by proteins in their membranes, although the precise nature of the protein-protein interactions underlying this are still uncertain [PUBMED:1976629]. Synaptobrevin may play a role in the molecular events underlying neurotransmitter release and vesicle recycling and may be involved in the regulation of membrane flow in the nerve terminal, a process mediated by interaction with low molecular weight GTP-binding proteins [PUBMED:8406010]. Synaptic vesicle-associated membrane proteins (VAMPs) from Torpedo californica (Pacific electric ray) and SNC1 from yeast are related to synaptobrevin.

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 has the following description:

The SNARE-fusion complex families are characterised by being tetrameric coiled-coil structures.

The clan 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
(111)
Full
(2176)
Representative proteomes NCBI
(2035)
Meta
(37)
RP15
(499)
RP35
(779)
RP55
(1125)
RP75
(1410)
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Format an alignment

  Seed
(111)
Full
(2176)
Representative proteomes NCBI
(2035)
Meta
(37)
RP15
(499)
RP35
(779)
RP55
(1125)
RP75
(1410)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

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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
(111)
Full
(2176)
Representative proteomes NCBI
(2035)
Meta
(37)
RP15
(499)
RP35
(779)
RP55
(1125)
RP75
(1410)
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.

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_303 (release 3.0)
Previous IDs: synaptobrevin;
Type: Family
Author: Finn RD, Bateman A
Number in seed: 111
Number in full: 2176
Average length of the domain: 80.20 aa
Average identity of full alignment: 29 %
Average coverage of the sequence by the domain: 38.98 %

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 25.0 25.0
Trusted cut-off 25.0 25.0
Noise cut-off 24.9 24.9
Model length: 89
Family (HMM) version: 16
Download: download the raw HMM for this family

Species distribution

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Interactions

There is 1 interaction for this family. More...

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 Synaptobrevin domain has been found. There are 40 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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