Summary: Bin/amphiphysin/Rvs domain for vesicular trafficking
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BAR domain Edit Wikipedia article
Structure of amphiphysin BAR.
BAR (Binâ€“Amphiphysinâ€“Rvs) domains are highly conserved protein dimerisation domains that occur in many proteins involved in membrane dynamics in a cell. The BAR domain is banana shaped and binds to membrane via its concave face. It is capable of sensing membrane curvature by binding preferentially to curved membranes.
BAR domains occur in combinations with other domains
Many BAR family proteins contain alternative lipid specificity domains that help target these protein to particular membrane compartments. Some also have SH3 domains that bind to dynamin and thus proteins like amphiphysin and endophilin are implicated in the orchestration of vesicle scission.
Some BAR domain containing proteins have an N-terminal amphipathic helix preceding the BAR domain. This helix inserts (like in the epsin ENTH domain) into the membrane and induces curvature, which is stabilised by the BAR dimer. Amphiphysin, endophilin, BRAP1/bin2 and nadrin are examples of such proteins containing an N-BAR. The Drosophila amphiphysin N-BAR (DA-N-BAR) is an example of a protein with a preference for negatively charged surfaces.
F-BAR (EFC) domain
F-BAR domains (for FCH-BAR, or EFC for Extended FCH Homology) are BAR domains that are extensions of the already established FCH domain. They are frequently found at the amino terminus of proteins. They can bind lipid membranes and can tubulate lipids in vitro and in vivo, but their exact physiological role still is under investigation. Examples of the F-BAR domain family are CIP4/FBP17/Toca-1 and Syndapins (also called PACSINs). Gene knock-out of syndapin I in mice revealed that that this brain-enriched isoform of the syndapin family is crucial for proper size control of synaptic vesicles and thereby indeed helps to define membrane curvature a physiological process. Work of the lab of Britta Qualmann also demonstrated that syndapin I is crucial for proper targeting of the large GTPase dynamin to membranes.
Human proteins containing this domain
- Peter BJ, Kent HM, Mills IG et al. (January 2004). "BAR domains as sensors of membrane curvature: the amphiphysin BAR structure". Science 303 (5657): 495â€“9. doi:10.1126/science.1092586. PMID 14645856.
- Qualmann B, Koch D, Kessels MM (August 2011). "Let's go bananas: revisiting the endocytic BAR code". EMBO J. 30 (17): 3501â€“15. doi:10.1038/emboj.2011.266. PMC 3181480. PMID 21878992.
- Koch D, Spiwoks-Becker I, Sabanov V, Sinning A, Dugladze T, Stellmacher A, Ahuja R, Grimm J, SchÃ¼ler S, MÃ¼ller A, Angenstein F, Ahmed T, Diesler A, Moser M, Tom Dieck S, Spessert R, Boeckers TM, FÃ¤ssler R, HÃ¼bner CA, Balschun D, Gloveli T, Kessels MM, Qualmann B (December 2011). "Proper synaptic vesicle formation and neuronal network activity critically rely on syndapin I". EMBO J. 30 (24): 4955â€“69. doi:10.1038/emboj.2011.339. PMC 3243622. PMID 21926968.
- Leventis PA, Chow BM, Stewart BA, Iyengar B, Campos AR, Boulianne GL (November 2001). "Drosophila Amphiphysin is a post-synaptic protein required for normal locomotion but not endocytosis". Traffic 2 (11): 839â€“50. doi:10.1034/j.1600-0854.2001.21113.x. PMID 11733051.
- Zhang B, Zelhof AC (July 2002). "Amphiphysins: raising the BAR for synaptic vesicle recycling and membrane dynamics. Bin-Amphiphysin-Rvsp". Traffic 3 (7): 452â€“60. doi:10.1034/j.1600-0854.2002.30702.x. PMID 12047553.Review.
- Zelhof AC, Bao H, Hardy RW, Razzaq A, Zhang B, Doe CQ (December 2001). "Drosophila Amphiphysin is implicated in protein localization and membrane morphogenesis but not in synaptic vesicle endocytosis". Development 128 (24): 5005â€“15. PMID 11748137.
- Mathew D, Popescu A, Budnik V (November 2003). "Drosophila amphiphysin functions during synaptic Fasciclin II membrane cycling". J. Neurosci. 23 (33): 10710â€“6. PMID 14627656.
- Peter BJ, Kent HM, Mills IG et al. (January 2004). "BAR domains as sensors of membrane curvature: the amphiphysin BAR structure". Science 303 (5657): 495â€“9. doi:10.1126/science.1092586. PMID 14645856.
- Weissenhorn W (August 2005). "Crystal structure of the endophilin-A1 BAR domain". J. Mol. Biol. 351 (3): 653â€“61. doi:10.1016/j.jmb.2005.06.013. PMID 16023669.
- Gallop JL, Jao CC, Kent HM et al. (June 2006). "Mechanism of endophilin N-BAR domain-mediated membrane curvature". EMBO J. 25 (12): 2898â€“910. doi:10.1038/sj.emboj.7601174. PMC 1500843. PMID 16763559.
- Masuda M, Takeda S, Sone M et al. (June 2006). "Endophilin BAR domain drives membrane curvature by two newly identified structure-based mechanisms". EMBO J. 25 (12): 2889â€“97. doi:10.1038/sj.emboj.7601176. PMC 1500852. PMID 16763557.
- Frost A, Perera R, Roux A et al. (March 2008). "Structural basis of membrane invagination by F-BAR domains". Cell 132 (5): 807â€“17. doi:10.1016/j.cell.2007.12.041. PMC 2384079. PMID 18329367.
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.
Bin/amphiphysin/Rvs domain for vesicular trafficking Provide feedback
This Pfam entry includes proteins that are not matched by PF03114.
Querin L, Sanvito R, Magni F, Busti S, Van Dorsselaer A, Alberghina L, Vanoni M; , J Biol Chem. 2007; [Epub ahead of print]: Proteomic analysis of a nutritional Shift-up in S. cerevisiae identifies Gvp36 as a BAR-containing protein involved in vesicular traffic and nutritional adaptation. PUBMED:18156177 EPMC:18156177
Internal database links
|SCOOP:||DUF2894 Casc1 BAR_3|
|Similarity to PfamA using HHSearch:||BAR|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR018859
Endocytosis and intracellular transport involve several mechanistic steps:
- (1) for the internalisation of cargo molecules, the membrane needs to bend to form a vesicular structure, which requires membrane curvature and a rearrangement of the cytoskeleton;
- (2) following its formation, the vesicle has to be pinched off the membrane;
- (3) the cargo has to be subsequently transported through the cell and the vesicle must fuse with the correct cellular compartment.
The crystal structure of these proteins suggest the domain forms a crescent-shaped dimer of a three-helix coiled coil with a characteristic set of conserved hydrophobic, aromatic and hydrophilic amino acids. Proteins containing this domain have been shown to homodimerise, heterodimerise or, in a few cases, interact with small GTPases.
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
The graphic that is shown by default represents the longest sequence with a given architecture. Each row contains the following information:
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This clan contains families that are involved in intracellular transport and signalling. Arfaptins are proteins which interact with small GTPases involved in vesicular budding at the Golgi complex. They form an elongated dimer of three helix coiled coils and are structurally very similar to the BAR domain . The Sec34 family is involved in tethering vesicles to the Golgi .
The clan contains the following 8 members:Arfaptin BAR BAR_2 BAR_3 BAR_3_WASP_bdg FAM92 IMD Vps5
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...
There are various ways to view or download the sequence alignments that we store. We provide several sequence viewers and a plain-text Stockholm-format file for download.
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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.
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
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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.
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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.
|Seed source:||Pfam-B_12557 (release 22.0)|
|Author:||Mistry J, Wood V|
|Number in seed:||10|
|Number in full:||400|
|Average length of the domain:||274.40 aa|
|Average identity of full alignment:||41 %|
|Average coverage of the sequence by the domain:||85.47 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||5|
|Download:||download the raw HMM for this family|
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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 More....
This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.
How the sunburst is generated
The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.
In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:
Colouring and labels
Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.
As you move your mouse across the sunburst, the current node will be highlighted. In the top section of the controls panel we show a summary of the lineage of the currently highlighed node. If you pause over an arc, a tooltip will be shown, giving the name of the taxonomic level in the title and a summary of the number of sequences and species below that node in the tree.
Anomalies in the taxonomy tree
There are some situations that the sunburst tree cannot easily handle and for which we have work-arounds in place.
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Some species in the taxonomic tree may not have one or more of the main eight levels that we display. For example, Bos taurus is not assigned an order in the NCBI taxonomic tree. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary.
Unmapped species names
The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".
Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
Too many species/sequences
For large species trees, you may see blank regions in the outer layers of the sunburst. These occur when there are large numbers of arcs to be drawn in a small space. If an arc is less than approximately one pixel wide, it will not be drawn and the space will be left blank. You may still be able to get some information about the species in that region by moving your mouse across the area, but since each arc will be very small, it will be difficult to accurately locate a particular species.
The tree shows the occurrence of this domain across different species. More...
We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.
Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.
If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.
For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.
We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.
Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.
We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.
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