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15  structures 137  species 5  interactions 5151  sequences 137  architectures

Family: PRY (PF13765)

Summary: SPRY-associated 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.

SPRY-associated domain Provide feedback

SPRY and PRY domains occur on PYRIN proteins. Their function is not known.

Literature references

  1. Stehlik C, Reed JC;, J Exp Med. 2004;200:551-558.: The PYRIN connection: novel players in innate immunity and inflammation. PUBMED:15353551 EPMC:15353551


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR006574

PRY is a domain associated with SPRY domains. The SPRY domain (INTERPRO) is of unknown function however distant homologues are domains in butyrophilin/marenostrin/pyrin. Ca2+-release from the sarcoplasmic or endoplasmic reticulum, the intracellular Ca2+ store, is mediated by the ryanodine receptor (RyR) and/or the inositol trisphosphate receptor (IP3R).

The proteins identified by the PRY domain, clearly fall into 3 sets which can be defined by their combination of signatures:

  • This group contains an immunoglobulin domain N-terminal to the PRY and butyrophilin domains. Butyrophilins are glycoproteins that are expressed on the apical surfaces of secretory cells in lactating mammary tissue and which may function in the secretion of milk-fat droplets.
  • This group contain a RING-finger domain N-terminal to the PRY domain. The RING-finger is a specialised type of Zn-finger of 40 to 60 residues that binds two atoms of zinc, and is probably involved in mediating protein-protein interactions. There are two different variants, the C3HC4-type and a C3H2C3-type, which is clearly related despite the different cysteine/histidine pattern. The latter type is sometimes referred to as 'RING-H2 finger' is not found associated with this group of proteins.

This set of proteins are described as TRIM (TRIpartite Motif) family members and are involved in cellular compartmentalisation [PUBMED:11331580]. The TRIM family sequences are defined by a Ring finger domain, a B-box type1 (B1) and a B-box type 2 (B2) followed by a coiled-coil (CC) region [PUBMED:1412709]. Genes belonging to this family are implicated in a variety of processes such as development and cell growth and are involved in human disease.

Many of these proteins, if not all of those with the PRY domain have a number of C-terminal signatures, SPRY, RFP-like (B30.2) and butyrophilin domain. The B30.2-like domain is a well conserved C-terminal domain of 160-170 amino acids which is found in nuclear and cytoplasmic proteins, as well as transmembrane and secreted proteins. The function of the B30.2-like domain is not known, but the cytoplasmic B30.2-like domain of butyrophilin has been shown to interact with xanthine oxidase [PUBMED:9866204].

The third set of proteins have the C-terminal signatures but have no N-terminal RING-finger or immunoglobulin domain signatures. These proteins have not been functionally described.

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 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
(150)
Full
(5151)
Representative proteomes NCBI
(8605)
Meta
(0)
RP15
(78)
RP35
(1142)
RP55
(2274)
RP75
(3066)
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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
(150)
Full
(5151)
Representative proteomes NCBI
(8605)
Meta
(0)
RP15
(78)
RP35
(1142)
RP55
(2274)
RP75
(3066)
Alignment:
Format:
Order:
Sequence:
Gaps:
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Download options

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
(150)
Full
(5151)
Representative proteomes NCBI
(8605)
Meta
(0)
RP15
(78)
RP35
(1142)
RP55
(2274)
RP75
(3066)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download    
Gzipped 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: Jackhmmer:B0V264
Previous IDs: none
Type: Family
Author: Coggill P
Number in seed: 150
Number in full: 5151
Average length of the domain: 48.80 aa
Average identity of full alignment: 37 %
Average coverage of the sequence by the domain: 9.58 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.5 27.5
Trusted cut-off 27.5 27.5
Noise cut-off 27.4 27.4
Model length: 49
Family (HMM) version: 2
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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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

There are 5 interactions for this family. More...

PRY SPRY RDM C1-set SPRY

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 PRY domain has been found. There are 15 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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