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14  structures 331  species 0  interactions 3647  sequences 37  architectures

Family: CD20 (PF04103)

Summary: CD20-like 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 "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
SymbolCD20
PfamPF04103
Pfam clanCL0347
InterProIPR007237
TCDB1.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

  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. CiteSeerX 10.1.1.326.2708. doi:10.1165/ajrcmb.20.2.3368. 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.

CD20-like family Provide feedback

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


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR007237

This entry includes B-lymphocyte antigen CD20 and other members of the membrane-spanning 4-domains subfamily A (MS4A), and closely related TMEM176 proteins [ PUBMED:20186339 , PUBMED:23874341 ]. It also includes sarcospan and some uncharacterised proteins.

The MS4A family includes the B-cell-specific antigen CD20, hematopoietic-cell-specific protein HTm4, high affinity IgE receptor beta chain (FceRIbeta), and related proteins [ PUBMED:11245982 ]. Members of this family have four putative transmembrane segments and are predominantly expressed in hematopoietic cells, with important roles in immunity [ PUBMED:11401424 ].

Sarcospan is a transmembrane component of dystrophin-glycoprotein complex (DGC), a complex that spans the muscle plasma membrane and forms a link between the F-actin cytoskeleton and the extracellular matrix. Sarcospan preferentially associates with the sarcoglycan subcomplex of the DGC. 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 6 members:

CD20 DUF2569 DUF4064 DUF4728 Mtp Tetraspanin

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...

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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
(37)
Full
(3647)
Representative proteomes UniProt
(5978)
RP15
(412)
RP35
(1021)
RP55
(2847)
RP75
(4104)
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PP/heatmap 1 View           

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

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

Format an alignment

  Seed
(37)
Full
(3647)
Representative proteomes UniProt
(5978)
RP15
(412)
RP35
(1021)
RP55
(2847)
RP75
(4104)
Alignment:
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Sequence:
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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
(37)
Full
(3647)
Representative proteomes UniProt
(5978)
RP15
(412)
RP35
(1021)
RP55
(2847)
RP75
(4104)
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_1979 (rel 7.3), Pfam-B_10092 (rel 9.0)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Bateman A , Moxon SJ , Pollington J , Finn RD
Number in seed: 37
Number in full: 3647
Average length of the domain: 129.10 aa
Average identity of full alignment: 19 %
Average coverage of the sequence by the domain: 43.66 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.9 27.9
Trusted cut-off 27.9 27.9
Noise cut-off 27.8 27.8
Model length: 156
Family (HMM) version: 17
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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Selections

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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 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 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
A0A087WRT7 View 3D Structure Click here
A0A087WSB9 View 3D Structure Click here
A0A087WSD2 View 3D Structure Click here
A0A0G2K3C3 View 3D Structure Click here
A0A0R4IHQ2 View 3D Structure Click here
A0A0R4IKD9 View 3D Structure Click here
A0A0R4IMA1 View 3D Structure Click here
A0A0R4IN69 View 3D Structure Click here
A0A0R4IZW2 View 3D Structure Click here
A0A2R8Q1B9 View 3D Structure Click here
A0A2R8Q8D5 View 3D Structure Click here
A0A2R8QQ76 View 3D Structure Click here
A5PM84 View 3D Structure Click here
A5PMI7 View 3D Structure Click here
A5WUU8 View 3D Structure Click here
A5WUU9 View 3D Structure Click here
A5WUV1 View 3D Structure Click here
A5WUV2 View 3D Structure Click here
B8A642 View 3D Structure Click here
B8A643 View 3D Structure Click here
D3Z8J6 View 3D Structure Click here
D3ZDZ2 View 3D Structure Click here
D3ZJ02 View 3D Structure Click here
D3ZSU4 View 3D Structure Click here
D3ZUX6 View 3D Structure Click here
D3ZZ58 View 3D Structure Click here
D4A4C7 View 3D Structure Click here
D4A4D6 View 3D Structure Click here
D4A4X2 View 3D Structure Click here
D4A4X2 View 3D Structure Click here
D4A4Y3 View 3D Structure Click here
D4A504 View 3D Structure Click here
D4A8R9 View 3D Structure Click here
D4ABT9 View 3D Structure Click here
E7F0M5 View 3D Structure Click here
E7FD05 View 3D Structure Click here
E9Q9V5 View 3D Structure Click here
E9QBB2 View 3D Structure Click here
E9QBH0 View 3D Structure Click here
E9QHI6 View 3D Structure Click here
F1LTM7 View 3D Structure Click here
F1LVJ1 View 3D Structure Click here
F1LZT4 View 3D Structure Click here
F1QPR7 View 3D Structure Click here
F1QSM6 View 3D Structure Click here
F1QTD0 View 3D Structure Click here
F1QWG5 View 3D Structure Click here
F1R2D6 View 3D Structure Click here
F6NRS7 View 3D Structure Click here
F6NXH3 View 3D Structure Click here
F6PCP4 View 3D Structure Click here
G3V955 View 3D Structure Click here
J3QN01 View 3D Structure Click here
M0R3W2 View 3D Structure Click here
M0R8F0 View 3D Structure Click here
M9PJS6 View 3D Structure Click here
O60320 View 3D Structure Click here
P11836 View 3D Structure Click here
P13386 View 3D Structure Click here
P19437 View 3D Structure Click here
P20490 View 3D Structure Click here
P81408 View 3D Structure Click here
Q01362 View 3D Structure Click here
Q14714 View 3D Structure Click here
Q1LVQ8 View 3D Structure Click here
Q3C1V0 View 3D Structure Click here
Q3UPL6 View 3D Structure Click here
Q3YBM2 View 3D Structure Click here
Q4G068 View 3D Structure Click here
Q5BLA7 View 3D Structure Click here
Q5FWC3 View 3D Structure Click here
Q5HZJ5 View 3D Structure Click here
Q5J8X5 View 3D Structure Click here
Q62147 View 3D Structure Click here
Q6A044 View 3D Structure Click here
Q810P8 View 3D Structure Click here
Q8N5U1 View 3D Structure Click here
Q920C4 View 3D Structure Click here
Q925D4 View 3D Structure Click here
Q95PZ5 View 3D Structure Click here
Q96DS6 View 3D Structure Click here
Q96HJ5 View 3D Structure Click here
Q96HP8 View 3D Structure Click here
Q96JA4 View 3D Structure Click here
Q96JQ5 View 3D Structure Click here
Q96PG1 View 3D Structure Click here
Q96PG2 View 3D Structure Click here
Q99N03 View 3D Structure Click here
Q99N05 View 3D Structure Click here
Q99N07 View 3D Structure Click here
Q99N08 View 3D Structure Click here
Q99N09 View 3D Structure Click here
Q99N10 View 3D Structure Click here
Q9BY19 View 3D Structure Click here
Q9D3F6 View 3D Structure Click here
Q9DCS1 View 3D Structure Click here
Q9ES61 View 3D Structure Click here
Q9GYM6 View 3D Structure Click here
Q9GZW8 View 3D Structure Click here
Q9H2W1 View 3D Structure Click here
Q9H3V2 View 3D Structure Click here
Q9NXJ0 View 3D Structure Click here
Q9R1Q6 View 3D Structure Click here
X1WC19 View 3D Structure Click here
X1WDL1 View 3D Structure Click here
X1WE70 View 3D Structure Click here
X1WEF3 View 3D Structure Click here