Summary: Regulated-SNARE-like 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.
Regulated-SNARE-like domain Provide feedback
Longin is one of the approximately 26 components required for transporting proteins from the ER to the plasma membrane, via the Golgi apparatus. It is necessary for the steps of the transfer from the ER to the Golgi complex [1]. Longins are the only R-SNAREs that are common to all eukaryotes, and they are characterised by a conserved N-terminal domain with a profilin-like fold called a longin domain [2].
Literature references
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Wen W, Chen L, Wu H, Sun X, Zhang M, Banfield DK; , Mol Biol Cell. 2006;17:4282-4299.: Identification of the yeast R-SNARE Nyv1p as a novel longin domain-containing protein. PUBMED:16855025 EPMC:16855025
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Rossi V, Banfield DK, Vacca M, Dietrich LE, Ungermann C, D'Esposito M, Galli T, Filippini F;, Trends Biochem Sci. 2004;29:682-688.: Longins and their longin domains: regulated SNAREs and multifunctional SNARE regulators. PUBMED:15544955 EPMC:15544955
This tab holds annotation information from the InterPro database.
InterPro entry IPR010908
VAMPs (and its homologue synaptobrevins) define a group of SNARE proteins that contain a C-terminal coiled-coil/SNARE domain, in combination with variable N-terminal domains that are used to classify VAMPs: those containing longin N-terminal domains (~150 aa) are referred to as longins, while those with shorter N-termini are referred to as brevins [ PUBMED:12914952 ]. Longins are the only type of VAMP protein found in all eukaryotes, suggesting that their longin domain is essential. The longin domain is thought to exert a regulatory function. Longin domains have been shown to share the same structural fold, a profilin-like globular domain consisting of a five-stranded antiparallel beta-sheet that is sandwiched by an alpha-helix on one side, and two alpha-helices on the other (beta(2)-alpha-beta(3)-alpha(2)).
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 PF (CL0431), which has the following description:
The families here all show the Profilin-like fold, and represent both the Profilin (actin-binding protein) (55770) and the Roadblock/LC7 domain-type (103196) superfamilies.
The clan contains the following 21 members:
Clat_adaptor_s FNIP_N Fuz_longin_1 Fuz_longin_2 Fuz_longin_3 Intu_longin_1 Intu_longin_2 Intu_longin_3 LAMTOR5 Longin Longin_2 MAPKK1_Int Nyv1_N Profilin Robl_LC7 Sedlin_N SLM4 SRP-alpha_N SRX Sybindin uDENNAlignments
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 (325) |
Full (7278) |
Representative proteomes | UniProt (12352) |
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RP15 (1241) |
RP35 (3504) |
RP55 (5789) |
RP75 (7791) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
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.
Seed (325) |
Full (7278) |
Representative proteomes | UniProt (12352) |
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RP15 (1241) |
RP35 (3504) |
RP55 (5789) |
RP75 (7791) |
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Raw Stockholm | |||||||
Gzipped |
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
Seed source: | Jackhmmer:C9J9A4 |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Coggill P |
Number in seed: | 325 |
Number in full: | 7278 |
Average length of the domain: | 81.60 aa |
Average identity of full alignment: | 25 % |
Average coverage of the sequence by the domain: | 34.66 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 84 | ||||||||||||
Family (HMM) version: | 8 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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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 Longin domain has been found. There are 32 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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