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19  structures 313  species 1  interaction 2173  sequences 82  architectures

Family: BAR (PF03114)

Summary: BAR domain

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BAR domain Edit Wikipedia article

BAR domain
PDB 1uru EBI.jpg
Structure of amphiphysin BAR.[1]
Identifiers
Symbol BAR
Pfam PF03114
InterPro IPR004148
SMART SM00721
PROSITE PDOC51021
SCOP 1uru
SUPERFAMILY 1uru
CDD cd07307

BAR (Bin–Amphiphysin–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[edit]

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.

N-BAR domain[edit]

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.[1]

F-BAR (EFC) domain[edit]

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 remains to be elucidated. Syndapin/pacsin proteins are an example of an F-BAR protein family.

Sorting nexins[edit]

The sorting nexin family of proteins includes several members that possess a BAR domain, including the well characterized SNX1 and SNX9.

Human proteins containing this domain[edit]

AMPH; ARHGAP17; BIN1; BIN2; BIN3; DNMBP; GMIP; RICH2; SH3BP1; SH3GL1; SH3GL2; SH3GL3; SH3GLB1; SH3GLB2;

See also[edit]

External links[edit]

References[edit]

  1. ^ a b Peter BJ, Kent HM, Mills IG, et al. (January 2004). "BAR domains as sensors of membrane curvature: the amphiphysin BAR structure". Science 303 (5657): 495–9. doi:10.1126/science.1092586. PMID 14645856. 

Publications[edit]

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.

BAR domain Provide feedback

BAR domains are dimerisation, lipid binding and curvature sensing modules found in many different protein families. A BAR domain with an additional N-terminal amphipathic helix (an N-BAR) can drive membrane curvature. These N-BAR domains are found in amphiphysin, endophilin, BRAP and Nadrin. BAR domains are also frequently found alongside domains that determine lipid specificity, like PF00169 and PF00787 domains in beta centaurins and sorting nexins respectively.

Literature references

  1. Gallop JL, Butler PJ, McMahon HT; , Nature. 2005;438:675-678.: Endophilin and CtBP/BARS are not acyl transferases in endocytosis or Golgi fission. PUBMED:16319893 EPMC:16319893

  2. Peter BJ, Kent HM, Mills IG, Vallis Y, Butler PJ, Evans PR, McMahon HT; , Science. 2004;303:495-499.: BAR domains as sensors of membrane curvature: the amphiphysin BAR structure. PUBMED:14645856 EPMC:14645856

  3. Gallop JL, Jao CC, Kent HM, Butler PJ, Evans PR, Langen R, McMahon HT; , EMBO J. 2006;25:2898-2910.: Mechanism of endophilin N-BAR domain-mediated membrane curvature. PUBMED:16763559 EPMC:16763559

  4. Weissenhorn W; , J Mol Biol. 2005;351:653-661.: Crystal structure of the endophilin-A1 BAR domain. PUBMED:16023669 EPMC:16023669


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR004148

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.
Members of the Amphiphysin protein family are key regulators in the early steps of endocytosis, involved in the formation of clathrin-coated vesicles by promoting the assembly of a protein complex at the plasma membrane and directly assist in the induction of the high curvature of the membrane at the neck of the vesicle. Amphiphysins contain a characteristic domain, known as the BAR (Bin-Amphiphysin-Rvs)-domain, which is required for their in vivo function and their ability to tubulate membranes [PUBMED:14993925].

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.

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 Golgi-transport (CL0145), which has the following description:

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 [1][2]. The Sec34 family is involved in tethering vesicles to the Golgi [3].

The clan contains the following 9 members:

Arfaptin BAR BAR_2 BAR_3_WASP_bdg FAM92 IMD Pil1 Sec34 Vps5

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...

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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
(28)
Full
(2173)
Representative proteomes NCBI
(2310)
Meta
(1)
RP15
(333)
RP35
(558)
RP55
(919)
RP75
(1287)
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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
(28)
Full
(2173)
Representative proteomes NCBI
(2310)
Meta
(1)
RP15
(333)
RP35
(558)
RP55
(919)
RP75
(1287)
Alignment:
Format:
Order:
Sequence:
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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
(28)
Full
(2173)
Representative proteomes NCBI
(2310)
Meta
(1)
RP15
(333)
RP35
(558)
RP55
(919)
RP75
(1287)
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: Psi-blast P25343
Previous IDs: none
Type: Domain
Author: Bateman A, McMahon HT
Number in seed: 28
Number in full: 2173
Average length of the domain: 214.10 aa
Average identity of full alignment: 18 %
Average coverage of the sequence by the domain: 40.80 %

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 24.5 24.5
Trusted cut-off 24.5 24.5
Noise cut-off 24.4 24.4
Model length: 230
Family (HMM) version: 13
Download: download the raw HMM for this family

Species distribution

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Interactions

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

BAR

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 BAR domain has been found. There are 19 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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