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14  structures 414  species 0  interactions 1064  sequences 13  architectures

Family: Calreticulin (PF00262)

Summary: Calreticulin family

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

This is the Wikipedia entry entitled "Calreticulin protein family". More...

Calreticulin protein family Edit Wikipedia article

Calreticulin
PDB 1k91 EBI.jpg
solution structure of calreticulin p-domain subdomain (residues 221-256)
Identifiers
Symbol Calreticulin
Pfam PF00262
InterPro IPR001580
PROSITE PDOC00636
SCOP 1jhn
SUPERFAMILY 1jhn

In molecular biology, the calreticulin protein family is a family of calcium-binding proteins. This family includes Calreticulin, Calnexin and Camlegin.[1][2][3]

References[edit]

  1. ^ Michalak M, Milner RE, Burns K, Opas M (August 1992). "Calreticulin". Biochem. J. 285 (3): 681–92. PMC 1132847. PMID 1497605. 
  2. ^ Bergeron JJ, Brenner MB, Thomas DY, Williams DB (March 1994). "Calnexin: a membrane-bound chaperone of the endoplasmic reticulum". Trends Biochem. Sci. 19 (3): 124–8. PMID 8203019. 
  3. ^ Watanabe D, Yamada K, Nishina Y, Tajima Y, Koshimizu U, Nagata A, Nishimune Y (March 1994). "Molecular cloning of a novel Ca(2+)-binding protein (calmegin) specifically expressed during male meiotic germ cell development". J. Biol. Chem. 269 (10): 7744–9. PMID 8126001. 

This article incorporates text from the public domain Pfam and InterPro IPR001580

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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.

Calreticulin family Provide feedback

No Pfam abstract.

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001580

Synonym(s): Calregulin, CRP55, HACBP

Calreticulin [PUBMED:1497605] is a high-capacity calcium-binding protein which is present in most tissues and located at the periphery of the endoplasmic (ER) and the sarcoplamic reticulum (SR) membranes. It probably plays a role in the storage of calcium in the lumen of the ER and SR and it may well have other important functions.

Structurally, calreticulin is a protein of about 400 amino acid residues consisting of three domains:

  • An N-terminal, probably globular, domain of about 180 amino acid residues (N-domain).
  • A central domain of about 70 residues (P-domain) which contains three repeats of an acidic 17 amino acid motif. This region binds calcium with a low-capacity, but a high-affinity.
  • A C-terminal domain rich in acidic residues and in lysine (C-domain). This region binds calcium with a high-capacity but a low-affinity.

Calreticulin is evolutionarily related to several other calcium-binding proteins, including Onchocerca volvulus antigen RAL-1, calnexin [PUBMED:8203019] and calmegin [PUBMED:8126001].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

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...

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
(68)
Full
(1064)
Representative proteomes NCBI
(1004)
Meta
(21)
RP15
(167)
RP35
(255)
RP55
(377)
RP75
(509)
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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
(68)
Full
(1064)
Representative proteomes NCBI
(1004)
Meta
(21)
RP15
(167)
RP35
(255)
RP55
(377)
RP75
(509)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

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
(68)
Full
(1064)
Representative proteomes NCBI
(1004)
Meta
(21)
RP15
(167)
RP35
(255)
RP55
(377)
RP75
(509)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

Pfam alignments:

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: Prosite
Previous IDs: calreticulin;
Type: Family
Author: Finn RD
Number in seed: 68
Number in full: 1064
Average length of the domain: 294.80 aa
Average identity of full alignment: 45 %
Average coverage of the sequence by the domain: 68.78 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 19.6 19.6
Trusted cut-off 20.6 20.1
Noise cut-off 18.7 19.0
Model length: 367
Family (HMM) version: 13
Download: download the raw HMM for this family

Species distribution

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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 Calreticulin domain has been found. There are 14 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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