Summary: RIH domain
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RIH domain Provide feedback
The RIH (RyR and IP3R Homology) domain is an extracellular domain from two types of calcium channels. This region is found in the ryanodine receptor P21817 and the inositol-1,4,5- trisphosphate receptor Q14571. This domain may form a binding site for IP3 [1].
Literature references
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Ponting CP; , Trends Biochem Sci 2000;25:48-50.: Novel repeats in ryanodine and IP3 receptors and protein O-mannosyltransferases. PUBMED:10664581 EPMC:10664581
External database links
SCOP: | 1n4k |
Transporter classification: | 1.A.3 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR000699
Ryanodine (RyR) and Inositol 1,4,5-trisphosphate (IP3) receptors are intracellular Ca2+-release channels. The RIH (RyR and IP3R Homology) domain is an extracellular domain from these two types of calcium channels. This domain may form a binding site for IP3 [PUBMED:10664581].
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Cellular component | membrane (GO:0016020) |
Molecular function | calcium channel activity (GO:0005262) |
Biological process | calcium ion transmembrane transport (GO:0070588) |
Domain organisation
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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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 (72) |
Full (3593) |
Representative proteomes | UniProt (5458) |
NCBI (13005) |
Meta (8) |
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RP15 (688) |
RP35 (1314) |
RP55 (2024) |
RP75 (2342) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
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not generated,
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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 (72) |
Full (3593) |
Representative proteomes | UniProt (5458) |
NCBI (13005) |
Meta (8) |
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RP15 (688) |
RP35 (1314) |
RP55 (2024) |
RP75 (2342) |
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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: | Ponting CP (EMBL alignments) |
Previous IDs: | none |
Type: | Family |
Sequence Ontology: | SO:0100021 |
Author: |
Bateman A |
Number in seed: | 72 |
Number in full: | 3593 |
Average length of the domain: | 192.20 aa |
Average identity of full alignment: | 27 % |
Average coverage of the sequence by the domain: | 10.75 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 203 | ||||||||||||
Family (HMM) version: | 21 | ||||||||||||
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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Interactions
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 RYDR_ITPR domain has been found. There are 308 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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