Summary: RIM-binding protein of the cytomatrix active zone
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RIM-binding protein of the cytomatrix active zone Provide feedback
This is a family of proteins that form part of the CAZ (cytomatrix at the active zone) complex which is involved in determining the site of synaptic vesicle fusion [1]. The C-terminus is a PDZ-binding motif that binds directly to RIM (a small G protein Rab-3A effector). The family also contains four coiled-coil domains [2].
Literature references
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Deguchi-Tawarada M, Inoue E, Takao-Rikitsu E, Inoue M, Ohtsuka T, Takai Y; , Genes Cells. 2004;9:15-23.: CAST2: identification and characterization of a protein structurally related to the presynaptic cytomatrix protein CAST. PUBMED:14723704 EPMC:14723704
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Wang Y, Liu X, Biederer T, Sudhof TC; , Proc Natl Acad Sci U S A. 2002;99:14464-14469.: A family of RIM-binding proteins regulated by alternative splicing: Implications for the genesis of synaptic active zones. PUBMED:12391317 EPMC:12391317
Internal database links
SCOOP: | AAA_13 Atg14 ATG16 Baculo_PEP_C CALCOCO1 CENP-F_leu_zip Crescentin EzrA Fez1 FPP GAS KASH_CCD Lebercilin MAD MscS_porin Myosin_tail_1 PKcGMP_CC Spc7 Tropomyosin Tropomyosin_1 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR019323
The active zone is the presynaptic region in the nerve terminals that mediates neurotransmitter release and is composed a dense collection of proteins called the cytomatrix at the active zone (CAZ). The CAZ proteins are thought to mediate synapse formation and regulate neurotransmitter release [PUBMED:22933801, PUBMED:24348337].
This entry represents the ELKS family, which are thought to be involved in the organisation of CAZ. Vertebrate ELKS proteins are produced by two genes, ERC1 and ERC2. Caenorhabditis elegans expresses a homologue of ELKS that acts downstream of syd2/liprin-alpha during active zone assembly [PUBMED:17115037]. Drosophila melanogaster expresses a related protein termed bruchpilot (brp) that consists of a conserved N terminus and a C-terminal half with no homologous sequences in vertebrates. Brp is required for structural integrity and function of synaptic active zones [PUBMED:16543132]. Vertebrate ELKS proteins are enriched at presynaptic active zones [PUBMED:16543132] and support Ca2+ influx at nerve terminals of inhibitory hippocampal neurons [PUBMED:25209271]. They have a C-terminal PDZ-binding motif that binds directly to RIM (a small G protein Rab-3A effector). These proteins also contain four coiled-coil domains [PUBMED:12391317].
Domain organisation
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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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, 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 (12) |
Full (1996) |
Representative proteomes | UniProt (3318) |
NCBI (7282) |
Meta (0) |
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RP15 (236) |
RP35 (536) |
RP55 (1253) |
RP75 (2040) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
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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 (12) |
Full (1996) |
Representative proteomes | UniProt (3318) |
NCBI (7282) |
Meta (0) |
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RP15 (236) |
RP35 (536) |
RP55 (1253) |
RP75 (2040) |
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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: | KOGs (KOG4809) |
Previous IDs: | none |
Type: | Coiled-coil |
Sequence Ontology: | SO:0001080 |
Author: |
KOGs, Finn RD |
Number in seed: | 12 |
Number in full: | 1996 |
Average length of the domain: | 441.10 aa |
Average identity of full alignment: | 37 % |
Average coverage of the sequence by the domain: | 65.77 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 763 | ||||||||||||
Family (HMM) version: | 10 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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