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35  structures 676  species 0  interactions 9031  sequences 126  architectures

Family: Copine (PF07002)

Summary: Copine

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

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.

Copine Provide feedback

This family represents a conserved region approximately 220 residues long within eukaryotic copines. Copines are Ca(2+)-dependent phospholipid-binding proteins that are thought to be involved in membrane-trafficking, and may also be involved in cell division and growth [1].

Literature references

  1. Tomsig JL, Creutz CE; , Cell Mol Life Sci 2002;59:1467-1477.: Copines: a ubiquitous family of Ca(2+)-dependent phospholipid-binding proteins. PUBMED:12440769 EPMC:12440769


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR010734

This represents a conserved region approximately 180 residues long within eukaryotic copines. Copines are Ca 2+ -dependent phospholipid-binding proteins that are thought to be involved in membrane-trafficking, and may also be involved in cell division and growth [ PUBMED:12440769 ]. They were originally identified in paramecium. They are found in human and orthologues have been found in C. elegans and Arabidopsis Thaliana. None have been found in D. Melanogaster or S. Cereviciae. Phylogenetic distribution suggests that copines have been lost in some eukaryotes [ PUBMED:9430674 ]. No functional properties have been assigned to the VWA domains present in copines. The members of this subgroup contain a functional MIDAS motif based on their preferential binding to magnesium and manganese. However, the MIDAS motif is not totally conserved, in most cases the MIDAS consists of the sequence DxTxS instead of the motif DxSxS that is found in most cases. The C2 domains present in copines mediate phospholipid binding [ PUBMED:12388743 , PUBMED:10830113 ].

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 vWA-like (CL0128), which has the following description:

To add.

The clan contains the following 19 members:

CobT_C Copine DUF1194 DUF2201 DUF444 DUF58 Integrin_beta ivWA Ku_N Med25_VWA Sec23_trunk Ssl1 Ste5_C Tfb4 VWA vWA-TerF-like VWA_2 VWA_3 VWA_CoxE

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 and the UniProtKB sequence database. More...

View options

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
(15)
Full
(9031)
Representative proteomes UniProt
(14169)
RP15
(1454)
RP35
(3602)
RP55
(7297)
RP75
(9416)
Jalview View  View  View  View  View  View  View 
HTML View             
PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(15)
Full
(9031)
Representative proteomes UniProt
(14169)
RP15
(1454)
RP35
(3602)
RP55
(7297)
RP75
(9416)
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
(15)
Full
(9031)
Representative proteomes UniProt
(14169)
RP15
(1454)
RP35
(3602)
RP55
(7297)
RP75
(9416)
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.

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: Pfam-B_9705 (release 10.0)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Vella Briffa B , Eberhardt R
Number in seed: 15
Number in full: 9031
Average length of the domain: 197.6 aa
Average identity of full alignment: 44 %
Average coverage of the sequence by the domain: 39.31 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.0 27.0
Trusted cut-off 27.0 27.0
Noise cut-off 26.9 26.9
Model length: 218
Family (HMM) version: 19
Download: download the raw HMM for this family

Species distribution

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Colour assignments

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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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 Copine domain has been found. There are 35 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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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A044TEV2 View 3D Structure Click here
A0A044TEZ7 View 3D Structure Click here
A0A044TTH8 View 3D Structure Click here
A0A044VIN3 View 3D Structure Click here
A0A077Z5W8 View 3D Structure Click here
A0A077ZL23 View 3D Structure Click here
A0A0H2UJT1 View 3D Structure Click here
A0A0H5S579 View 3D Structure Click here
A0A0J9XTX2 View 3D Structure Click here
A0A0K0E652 View 3D Structure Click here
A0A0K0EP16 View 3D Structure Click here
A0A0K0EP72 View 3D Structure Click here
A0A0N4U4X4 View 3D Structure Click here
A0A0N4URS0 View 3D Structure Click here
A0A0P0WLH0 View 3D Structure Click here
A0A0P0XBN7 View 3D Structure Click here
A0A0P0XRG8 View 3D Structure Click here
A0A0R0G4C4 View 3D Structure Click here
A0A0R0IN04 View 3D Structure Click here
A0A0R0IR54 View 3D Structure Click here
A0A0R4IS92 View 3D Structure Click here
A0A158Q489 View 3D Structure Click here
A0A158Q4S3 View 3D Structure Click here
A0A1D6EM25 View 3D Structure Click here
A0A1D6EN69 View 3D Structure Click here
A0A1D6ET46 View 3D Structure Click here
A0A1D6FUM5 View 3D Structure Click here
A0A1D6G420 View 3D Structure Click here
A0A1D6G6M1 View 3D Structure Click here
A0A1D6H144 View 3D Structure Click here
A0A1D6H9B3 View 3D Structure Click here
A0A1D6L5R0 View 3D Structure Click here
A0A1D6LF18 View 3D Structure Click here
A0A1D6LS17 View 3D Structure Click here
A0A1D6MV70 View 3D Structure Click here
A0A1D6N3Y9 View 3D Structure Click here
A0A1D6PQ30 View 3D Structure Click here
A0A1P8AWA7 View 3D Structure Click here
A0A286Y928 View 3D Structure Click here
A0A2K6VHV9 View 3D Structure Click here