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4  structures 113  species 0  interactions 1022  sequences 9  architectures

Family: CD20 (PF04103)

Summary: CD20-like family

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This is the Wikipedia entry entitled "CD20-like family". More...

CD20-like family Edit Wikipedia article

CD20-like family
PDB 2osl EBI.jpg
crystal structure of rituximab fab in complex with an epitope peptide
Identifiers
Symbol CD20
Pfam PF04103
Pfam clan CL0347
InterPro IPR007237
TCDB 1.A.37

In molecular biology, the CD20-like family of proteins includes the CD20 protein and the beta subunit of the high affinity receptor for IgE Fc, MS4A2. MS4A2 has a tetrameric structure consisting of a single IgE-binding alpha subunit, a single beta subunit, and two disulfide-linked gamma subunits. It has four putative transmembrane segments and a probable topology where both amino- and carboxy termini protrude into the cytoplasm.[1] This family also includes LR8 like proteins from humans (TMEM176B), mice and rats. The function of the human LR8 protein is unknown although it is known to be strongly expressed in the lung fibroblasts.[2] This family also includes sarcospan, a transmembrane component of dystrophin-associated glycoprotein. Loss of the sarcoglycan complex and sarcospan alone is sufficient to cause muscular dystrophy. The role of the sarcoglycan complex and sarcospan is thought to be to strengthen the dystrophin axis connecting the basement membrane with the cytoskeleton.[3]

References[edit]

  1. ^ Hupp K, Siwarski D, Mock BA, Kinet JP (December 1989). "Gene mapping of the three subunits of the high affinity FcR for IgE to mouse chromosomes 1 and 19". J. Immunol. 143 (11): 3787–91. PMID 2531187. 
  2. ^ Lurton J, Rose TM, Raghu G, Narayanan AS (February 1999). "Isolation of a gene product expressed by a subpopulation of human lung fibroblasts by differential display". Am. J. Respir. Cell Mol. Biol. 20 (2): 327–31. PMID 9922225. 
  3. ^ Araishi K, Sasaoka T, Imamura M, Noguchi S, Hama H, Wakabayashi E, Yoshida M, Hori T, Ozawa E (September 1999). "Loss of the sarcoglycan complex and sarcospan leads to muscular dystrophy in beta-sarcoglycan-deficient mice". Hum. Mol. Genet. 8 (9): 1589–98. doi:10.1093/hmg/8.9.1589. PMID 10441321. 

This article incorporates text from the public domain Pfam and InterPro IPR007237

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.

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This family includes the CD20 protein and the beta subunit of the high affinity receptor for IgE Fc. The high affinity receptor for IgE is a tetrameric structure consisting of a single IgE-binding alpha subunit, a single beta subunit, and two disulfide-linked gamma subunits. The alpha subunit of Fc epsilon RI and most Fc receptors are homologous members of the Ig superfamily. By contrast, the beta and gamma subunits from Fc epsilon RI are not homologous to the Ig superfamily. Both molecules have four putative transmembrane segments and a probably topology where both amino- and carboxy termini protrude into the cytoplasm [1]. This family also includes LR8 like proteins from humans, mice and rats. The function of the human LR8 protein is unknown although it is known to be strongly expressed in the lung fibroblasts [2]. This family also includes sarcospan is a transmembrane component of dystrophin-associated glycoprotein. Loss of the sarcoglycan complex and sarcospan alone is sufficient to cause muscular dystrophy. The role of the sarcoglycan complex and sarcospan is thought to be to strengthen the dystrophin axis connecting the basement membrane with the cytoskeleton [3].

Literature references

  1. Hupp K, Siwarski D, Mock BA, Kinet JP; , J Immunol 1989;143:3787-3791.: Gene mapping of the three subunits of the high affinity FcR for IgE to mouse chromosomes 1 and 19. PUBMED:2531187 EPMC:2531187

  2. Lurton J, Rose TM, Raghu G, Narayanan AS; , Am J Respir Cell Mol Biol 1999;20:327-331.: Isolation of a gene product expressed by a subpopulation of human lung fibroblasts by differential display. PUBMED:9922225 EPMC:9922225

  3. Araishi K, Sasaoka T, Imamura M, Noguchi S, Hama H, Wakabayashi E, Yoshida M, Hori T, Ozawa E; , Hum Mol Genet. 1999;8:1589-1598.: Loss of the sarcoglycan complex and sarcospan leads to muscular dystrophy in beta-sarcoglycan-deficient mice. PUBMED:10441321 EPMC:10441321


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR007237

This family includes the CD20 protein and the beta subunit of the high affinity receptor for IgE Fc. The high affinity receptor for IgE is a tetrameric structure consisting of a single IgE-binding alpha subunit, a single beta subunit, and two disulphide-linked gamma subunits. The alpha subunit of Fc epsilon RI and most Fc receptors are homologous members of the Ig superfamily. By contrast, the beta and gamma subunits from Fc epsilon RI are not homologous to the Ig superfamily. Both molecules have four putative transmembrane segments and a probably topology where both amino- and carboxy termini protrude into the cytoplasm [PUBMED:2531187]. This family also includes LR8 like proteins from humans, mice and rats. The function of the human LR8 protein is unknown although it is known to be strongly expressed in the lung fibroblasts [PUBMED:9922225]. This family also includes sarcospan is a transmembrane component of dystrophin-associated glycoprotein. Loss of the sarcoglycan complex and sarcospan alone is sufficient to cause muscular dystrophy. The role of the sarcoglycan complex and sarcospan is thought to be to strengthen the dystrophin axis connecting the basement membrane with the cytoskeleton [PUBMED:10441321].

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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Pfam Clan

This family is a member of clan Tetraspannin (CL0347), which has the following description:

This clan includes the tetraspanin family which contains four transmembrane regions. The CD20 family also has four transmembrane regions, but its members are not considered true tetraspanins as they lack nearly all of the key functional tetraspanin residues [1].

The clan contains the following 3 members:

CD20 DUF4064 Tetraspannin

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
(80)
Full
(1022)
Representative proteomes NCBI
(1008)
Meta
(0)
RP15
(125)
RP35
(173)
RP55
(258)
RP75
(533)
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Format an alignment

  Seed
(80)
Full
(1022)
Representative proteomes NCBI
(1008)
Meta
(0)
RP15
(125)
RP35
(173)
RP55
(258)
RP75
(533)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(80)
Full
(1022)
Representative proteomes NCBI
(1008)
Meta
(0)
RP15
(125)
RP35
(173)
RP55
(258)
RP75
(533)
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: Pfam-B_1979 (rel 7.3), Pfam-B_10092 (rel 9.0)
Previous IDs: none
Type: Family
Author: Bateman A, Moxon SJ, Pollington J, Finn RD
Number in seed: 80
Number in full: 1022
Average length of the domain: 133.70 aa
Average identity of full alignment: 19 %
Average coverage of the sequence by the domain: 47.50 %

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 26.3 26.3
Trusted cut-off 26.3 26.3
Noise cut-off 26.2 26.2
Model length: 150
Family (HMM) version: 10
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 CD20 domain has been found. There are 4 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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