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8  structures 83  species 0  interactions 275  sequences 11  architectures

Family: ECD (PF18432)

Summary: Extracellular Cadherin domain

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 "Cadherin". More...

Cadherin Edit Wikipedia article

Principal interactions of structural proteins at cadherin-based adherens junction. Actin filaments are linked to α-actinin and to membrane through vinculin. The head domain of vinculin associates to E-cadherin via α-, β-, and γ-catenins. The tail domain of vinculin binds to membrane lipids and to actin filaments.

Cadherins (named for "calcium-dependent adhesion") are a type of cell adhesion molecule (CAM) that is important in the formation of adherens junctions to bind cells with each other.[1] Cadherins are a class of type-1 transmembrane proteins. They are dependent on calcium (Ca2+) ions to function, hence their name. Cell-cell adhesion is mediated by extracellular cadherin domains, whereas the intracellular cytoplasmic tail associates with a large number of adaptor and signaling proteins, collectively referred to as the cadherin adhesome.

The cadherin superfamily includes cadherins, protocadherins, desmogleins, and desmocollins, and more.[2][3] In structure, they share cadherin repeats, which are the extracellular Ca2+-binding domains. There are multiple classes of cadherin molecule, each designated with a prefix (in general, noting the type of tissue with which it is associated). It has been observed that cells containing a specific cadherin subtype tend to cluster together to the exclusion of other types, both in cell culture and during development.[4] For example, cells containing N-cadherin tend to cluster with other N-cadherin-expressing cells. However, it has been noted that the mixing speed in the cell culture experiments can have an effect on the extent of homotypic specificity.[5] In addition, several groups have observed heterotypic binding affinity (i.e., binding of different types of cadherin together) in various assays.[6][7] One current model proposes that cells distinguish cadherin subtypes based on kinetic specificity rather than thermodynamic specificity, as different types of cadherin homotypic bonds have different lifetimes.[8]

Structure and function

Cadherins are synthesized as polypeptides and undergo many post-translational modifications to become the proteins which mediate cell-cell adhesion and recognition.[9] These polypeptides are approximately 720–750 amino acids long. Each cadherin has a small cytoplasmic component, a transmembrane component, and the remaining bulk of the protein is extra-cellular (outside the cell). The transmembrane component consists of single chain glycoprotein repeats.[10]  Because cadherins are Ca2+ dependent, they have five tandem extracellular domain repeats that act as the binding site for Ca2+ ions.[11]  Their extracellular domain interacts in two separate trans dimer conformations: strand-swap dimers (S-dimers) and X-dimers.[11] To date, over 100 types of cadherins in humans have been identified and sequenced.[12]

 The functionality of cadherins relies upon the formation of two identical subunits, known as homodimers.[10] The homodimeric cadherins create cell-cell adhesion with cadherins present in the membranes of other cells through changing conformation from cis-dimers to trans-dimers.[10] Once the cell-cell adhesion between cadherins present in the cell membranes of two different cells has formed, adherens junctions can then be made when protein complexes, usually composed of α-, β-, and γ-catenins, bind to the actin cytoskeleton portion of the cadherin.[10]

Development

Cadherins behave as both receptors and ligands for other molecules. During development, their behavior assists in properly positioning cells: they are responsible for the separation of the different tissue layers, and for cellular migration.[13] In the very early stages of development, E-cadherin (epithelial cadherin) is most greatly expressed. Many cadherins are specified for specific functions in the cell, and they are differentially expressed in a developing embryo. For example, during neurulation, when the neural plate is forming in the embryo, the tissues residing near the cranial neural folds have decreased N-cadherin expression.[14] Conversely, the expression of the N-cadherins remains unchanged in the other regions of the neural tube that is located on the anterior-posterior axis of the vertebrate.[14] The expression of the different types of cadherins in the cell are varying dependent upon the specific differentiation and specification of the organism during development.

Cadherins play a vital role in the migration of cells through the epithelial-mesenchymal transition (EMT), which requires cadherins to forms adherents junctions with neighboring cells. In neural crest cells, which are transient cells that arise in the developing organism during gastrulation and function in the patterning of the vertebrate body plan, the cadherins are necessary to allow migration of cells to form tissues or organs.[14] In addition, cadherins responsible in the EMT event in early development have also been shown to be critical in the reprogramming of specified adult cells into a pluripotent state, forming induced pluripotent stem cells (iPSCs).[1]

After development, cadherins play a role in maintaining cell and tissue structure, and in cellular movement.[12] Regulation of cadherin expression can occur through promoter methylation among other epigenetic mechanisms.[15]

Tumour metastasis

The E-cadherin–catenin complex plays a key role in cellular adhesion; loss of this function has been associated with greater tumour metastasis.[16]

Types

Cadherin domain
Identifiers
Symbol Cadherin
Pfam PF00028
InterPro IPR002126
SMART CA
PROSITE PDOC00205
SCOP 1nci
SUPERFAMILY 1nci
Ribbon representation of a repeating unit in the extracellular E-cadherin ectodomain of the mouse (Mus musculus) [17]

There are said to be over 100 different types of cadherins found in vertebrates, which can be classified into four groups: classical, desmosomal, protocadherins, and unconventional.[18][19] This large amount of diversity is accomplished by having multiple cadherin encoding genes combined with alternative RNA splicing mechanisms. Invertebrates contain fewer than 20 types of cadherins.[19]

Classical

Different members of the cadherin family are found in different locations.

  • CDH1 – E-cadherin (epithelial): E-cadherins are found in epithelial tissue
  • CDH2 – N-cadherin (neural): N-cadherins are found in neurons
  • CDH12 – cadherin 12, type 2 (N-cadherin 2)
  • CDH3 – P-cadherin (placental): P-cadherins are found in the placenta.

Desmosomal

Protocadherins

PCDH15; PCDH17; PCDH18; PCDH19; PCDH20; PCDH7; PCDH8; PCDH9; PCDHA1; PCDHA10; PCDHA11; PCDHA12; PCDHA13; PCDHA2; PCDHA3; PCDHA4; PCDHA5; PCDHA6; PCDHA7; PCDHA8; PCDHA9; PCDHAC1; PCDHAC2; PCDHB1; PCDHB10; PCDHB11; PCDHB12; PCDHB13; PCDHB14; PCDHB15; PCDHB16; PCDHB17; PCDHB18; PCDHB2; PCDHB3; PCDHB4; PCDHB5; PCDHB6; PCDHB7; PCDHB8; PCDHB9; PCDHGA1; PCDHGA10; PCDHGA11; PCDHGA12; PCDHGA2; PCDHGA3; PCDHGA4; PCDHGA5; PCDHGA6; PCDHGA7; PCDHGA8; PCDHGA9; PCDHGB1; PCDHGB2; PCDHGB3; PCDHGB4; PCDHGB5; PCDHGB6; PCDHGB7; PCDHGC3; PCDHGC4; PCDHGC5

FAT; FAT2; FAT4;

Unconventional/ungrouped

  • CDH9 – cadherin 9, type 2 (T1-cadherin)
  • CDH10 – cadherin 10, type 2 (T2-cadherin)
  • CDH4 – R-cadherin (retinal)
  • CDH5 – VE-cadherin (vascular endothelial)
  • CDH6 – K-cadherin (kidney)
  • CDH7 – cadherin 7, type 2
  • CDH8 – cadherin 8, type 2
  • CDH11 – OB-cadherin (osteoblast)
  • CDH13 – T-cadherin – H-cadherin (heart)
  • CDH15 – M-cadherin (myotubule)
  • CDH16 – KSP-cadherin
  • CDH17 – LI cadherin (liver-intestine)
  • CDH18 – cadherin 18, type 2
  • CDH19 – cadherin 19, type 2
  • CDH20 – cadherin 20, type 2
  • CDH23 – cadherin 23 (neurosensory epithelium)
  • CDH10; CDH11; CDH13; CDH15; CDH16; CDH17;

CDH18; CDH19; CDH20; CDH22; CDH23; CDH24; CDH26; CDH28; CDH4; CDH5; CDH6; CDH7; CDH8; CDH9;

CELSR1; CELSR2; CELSR3; CLSTN1; CLSTN2; CLSTN3; DCHS1; DCHS2; LOC389118;

See also

References

  1. ^ a b Alimperti, Stella; Andreadis, Stelios T. "CDH2 and CDH11 act as regulators of stem cell fate decisions". Stem Cell Research. 14 (3): 270–282. doi:10.1016/j.scr.2015.02.002. 
  2. ^ Hulpiau P, van Roy F (February 2009). "Molecular evolution of the cadherin superfamily". Int. J. Biochem. Cell Biol. 41 (2): 349–69. doi:10.1016/j.biocel.2008.09.027. PMID 18848899. 
  3. ^ Angst B, Marcozzi C, Magee A (February 2001). "The cadherin superfamily: diversity in form and function". J Cell Sci. 114 (Pt 4): 629–41. PMID 11171368. 
  4. ^ Bello, S.M.; Millo, H.; Rajebhosale, M.; Price, S.R. (2012). "Catenin-dependent cadherin function drives divisional segregation of spinal chord motor neurons". Journal of Neuroscience. 32 (2): 490–505. doi:10.1523/jneurosci.4382-11.2012. 
  5. ^ Duguay, D.; A. Foty R., RA; S. Steinberg M., MS (2003). "Cadherin-mediated cell adhesion and tissue segregation: qualitative and quantitative determinants". Dev. Biol. 253 (2): 309–323. doi:10.1016/S0012-1606(02)00016-7. PMID 12645933. 
  6. ^ Niessen, Carien M.; Gumbiner, Barry M. (2002). "Cadherin-mediated cell sorting not determined by binding or adhesion specificity". The Journal of Cell Biology. 156 (2): 389–399. doi:10.1083/jcb.200108040. PMC 2199232Freely accessible. PMID 11790800. 
  7. ^ Volk, T.; Cohen, O.; Geiger, B. (1987). "Formation of heterotypic adherens-type junctions between L-CAM containing liver cells and A-CAM containing lens cells". Cell. 50 (6): 987–994. doi:10.1016/0092-8674(87)90525-3. PMID 3621349. 
  8. ^ Bayas, Marco V.; Leung, Andrew; Evans, Evan; Leckband, Deborah (2005). "Lifetime Measurements Reveal Kinetic Differences between Homophilic Cadherin Bonds". Biophysical Journal. 90 (4): 1385–95. doi:10.1529/biophysj.105.069583. PMC 1367289Freely accessible. PMID 16326909. 
  9. ^ Harris, T. J.; Tepass, U (2010). "Adherens junctions: From molecules to morphogenesis". Nature Reviews Molecular Cell Biology. 11 (7): 502–14. doi:10.1038/nrm2927. PMID 20571587. 
  10. ^ a b c d Marie, Pierre J.; Haÿ, Eric; Modrowski, Dominique; Revollo, Leila; Mbalaviele, Gabriel; Civitelli, Roberto (2014-01-01). "Cadherin-Mediated Cell–Cell Adhesion and Signaling in the Skeleton". Calcified Tissue International. 94 (1): 46–54. doi:10.1007/s00223-013-9733-7. ISSN 0171-967X. PMC 4272239Freely accessible. 
  11. ^ a b Priest, Andrew Vae; Shafraz, Omer; Sivasankar, Sanjeevi. "Biophysical basis of cadherin mediated cell-cell adhesion". Experimental Cell Research. 358 (1): 10–13. doi:10.1016/j.yexcr.2017.03.015. 
  12. ^ a b Tepass, U; Truong, K; Godt, D; Ikura, M; Peifer, M (2000). "Cadherins in embryonic and neural morphogenesis". Nature Reviews Molecular Cell Biology. 1 (2): 91–100. doi:10.1038/35040042. PMID 11253370. 
  13. ^ Gumbiner, B. M. (2005). "Regulation of cadherin-mediated adhesion in morphogenesis". Nature Reviews Molecular Cell Biology. 6 (8): 622–34. doi:10.1038/nrm1699. PMID 16025097. 
  14. ^ a b c Taneyhill, Lisa A.; Schiffmacher, Andrew T. (2017-06-01). "Should I stay or should I go? Cadherin function and regulation in the neural crest". genesis. 55 (6): n/a–n/a. doi:10.1002/dvg.23028. ISSN 1526-968X. 
  15. ^ Reinhold, WC; Reimers, MA; Maunakea, AK; Kim, S; Lababidi, S; Scherf, U; Shankavaram, UT; Ziegler, MS; Stewart, C; Kouros-Mehr, Hosein; Cui, H; Dolginow, D; Scudiero, DA; Pommier, YG; Munroe, DJ; Feinberg, AP; Weinstein, JN (Feb 2007). "Detailed DNA methylation profiles of the E-cadherin promoter in the NCI-60 cancer cells". Molecular cancer therapeutics. 6 (2): 391–403. doi:10.1158/1535-7163.MCT-06-0609. PMID 17272646. 
  16. ^ Beavon, IR (August 2000). "The E-cadherin-catenin complex in tumour metastasis: structure, function and regulation". European Journal of Cancer. 36 (13 Spec No): 1607–20. doi:10.1016/S0959-8049(00)00158-1. PMID 10959047. 
  17. ^ PDB: 3Q2V​; Harrison, O.J.; Jin, X.; Hong, S.; Bahna, F.; Ahlsen, G.; Brasch, J.; Wu, Y.; Vendome, J.; Felsovalyi, K.; Hampton, C.M.; Troyanovsky, R.B.; Ben-Shaul, A.; Frank, J.; Troyanovsky, S.M.; Shapiro, L.; Honig, B. (2011). "The extracellular architecture of adherens junctions revealed by crystal structures of type I cadherins". Structure. 19 (2): 244–56. doi:10.1016/j.str.2010.11.016. PMC 3070544Freely accessible. PMID 21300292. ; rendered with PyMOL
  18. ^ Stefan Offermanns; Walter Rosenthal (2008). Encyclopedia of Molecular Pharmacology. Springer. pp. 306–. ISBN 978-3-540-38916-3. Retrieved 14 December 2010. 
  19. ^ a b Lodish, Harvey; Berk, Arnold; Kaiser, Chris; Krieger, Monte; Bretscher, Anthony; Ploegh, Hidde; Amon, Angelika (2013). Molecular Cell Biology (Seventh ed.). New York: Worth Publ. p. 934. ISBN 978-1-4292-3413-9. 

Further reading

  • Beavon IR (2000). "The E-cadherin-catenin complex in tumour metastasis: structure, function and regulation". Eur. J. Cancer. 36 (13 Spec No): 1607–20. doi:10.1016/S0959-8049(00)00158-1. PMID 10959047. 
  • Berx G, Becker KF, Höfler H, van Roy F (1998). "Mutations of the human E-cadherin (CDH1) gene". Hum. Mutat. 12 (4): 226–37. doi:10.1002/(SICI)1098-1004(1998)12:4<226::AID-HUMU2>3.0.CO;2-D. PMID 9744472. 
  • Bryant DM, Stow JL (2005). "The ins and outs of E-cadherin trafficking". Trends Cell Biol. 14 (8): 427–34. doi:10.1016/j.tcb.2004.07.007. PMID 15308209. 
  • Chun YS, Lindor NM, Smyrk TC, et al. (2001). "Germline E-cadherin gene mutations: is prophylactic total gastrectomy indicated?". Cancer. 92 (1): 181–7. doi:10.1002/1097-0142(20010701)92:1<181::AID-CNCR1307>3.0.CO;2-J. PMID 11443625. 
  • Georgolios A, Batistatou A, Manolopoulos L, Charalabopoulos K (2006). "Role and expression patterns of E-cadherin in head and neck squamous cell carcinoma (HNSCC)". J. Exp. Clin. Cancer Res. 25 (1): 5–14. PMID 16761612. 
  • Hazan RB, Qiao R, Keren R, et al. (2004). "Cadherin switch in tumor progression". Ann. N. Y. Acad. Sci. 1014 (1): 155–63. doi:10.1196/annals.1294.016. PMID 15153430. 
  • Moran CJ, Joyce M, McAnena OJ (2005). "CDH1 associated gastric cancer: a report of a family and review of the literature". Eur J Surg Oncol. 31 (3): 259–64. doi:10.1016/j.ejso.2004.12.010. PMID 15780560. 
  • Reynolds AB, Carnahan RH (2005). "Regulation of cadherin stability and turnover by p120ctn: implications in disease and cancer". Semin. Cell Dev. Biol. 15 (6): 657–63. doi:10.1016/j.semcdb.2004.09.003. PMID 15561585. 
  • Wang HD, Ren J, Zhang L (2004). "CDH1 germline mutation in hereditary gastric carcinoma". World J. Gastroenterol. 10 (21): 3088–93. PMID 15457549. 
  • Wijnhoven BP, Dinjens WN, Pignatelli M (2000). "E-cadherin-catenin cell-cell adhesion complex and human cancer". The British journal of surgery. 87 (8): 992–1005. doi:10.1046/j.1365-2168.2000.01513.x. PMID 10931041. 
  • Wilson PD (2001). "Polycystin: new aspects of structure, function, and regulation". J. Am. Soc. Nephrol. 12 (4): 834–45. PMID 11274246. 
  • Renaud-Young M, Gallin WJ (2002). "In the first extracellular domain of E-cadherin, heterophilic interactions, but not the conserved His-Ala-Val motif, are required for adhesion". Journal of Biological Chemistry. 277 (42): 39609–39616. doi:10.1074/jbc.M201256200. PMID 12154084. 

External links

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

This is the Wikipedia entry entitled "PCDH15". More...

PCDH15 Edit Wikipedia article

PCDH15
Available structures
PDB Ortholog search: PDBe RCSB
Identifiers
Aliases PCDH15, CDHR15, DFNB23, USH1F, protocadherin-related 15, protocadherin related 15
External IDs MGI: 1891428 HomoloGene: 23401 GeneCards: PCDH15
Gene location (Human)
Chromosome 10 (human)
Chr. Chromosome 10 (human)[1]
Chromosome 10 (human)
Genomic location for PCDH15
Genomic location for PCDH15
Band 10q21.1 Start 53,802,771 bp[1]
End 55,627,942 bp[1]
Orthologs
Species Human Mouse
Entrez
Ensembl
UniProt
RefSeq (mRNA)
RefSeq (protein)
Location (UCSC) Chr 10: 53.8 – 55.63 Mb Chr 10: 73.1 – 74.65 Mb
PubMed search [3] [4]
Wikidata
View/Edit Human View/Edit Mouse

Protocadherin-15 is a protein that in humans is encoded by the PCDH15 gene.[5][6][7]

Function

This gene is a member of the cadherin superfamily. Family members encode integral membrane proteins that mediate calcium-dependent cell-cell adhesion. The protein product of this gene consists of a signal peptide, 11 extracellular calcium-binding domains, a transmembrane domain and a unique cytoplasmic domain. It plays an essential role in maintenance of normal retinal and cochlear function.[7] It is thought to interact with CDH23 to form tip-link filaments.[8]

Clinical significance

Mutations in this gene have been associated with hearing loss, which is consistent with its location at the Usher syndrome type 1F (USH1F) critical region on chromosome 10.[7] Variation within it has also been found to be associated with normal differences in human facial appearance.[9]

References

  1. ^ a b c GRCh38: Ensembl release 89: ENSG00000150275 - Ensembl, May 2017
  2. ^ a b c GRCm38: Ensembl release 89: ENSMUSG00000052613 - Ensembl, May 2017
  3. ^ "Human PubMed Reference:". 
  4. ^ "Mouse PubMed Reference:". 
  5. ^ Ahmed ZM, Riazuddin S, Bernstein SL, Ahmed Z, Khan S, Griffith AJ, Morell RJ, Friedman TB, Riazuddin S, Wilcox ER (Jun 2001). "Mutations of the protocadherin gene PCDH15 cause Usher syndrome type 1F". Am J Hum Genet. 69 (1): 25–34. doi:10.1086/321277. PMC 1226045Freely accessible. PMID 11398101. 
  6. ^ Ahmed ZM, Riazuddin S, Ahmad J, Bernstein SL, Guo Y, Sabar MF, Sieving P, Riazuddin S, Griffith AJ, Friedman TB, Belyantseva IA, Wilcox ER (Dec 2003). "PCDH15 is expressed in the neurosensory epithelium of the eye and ear and mutant alleles are responsible for both USH1F and DFNB23". Hum Mol Genet. 12 (24): 3215–23. doi:10.1093/hmg/ddg358. PMID 14570705. 
  7. ^ a b c "Entrez Gene: PCDH15 protocadherin 15". 
  8. ^ Kazmierczak, Piotr; Sakaguchi, Hirofumi; Tokita, Joshua; Wilson-Kubalek, Elizabeth M.; Milligan, Ronald A.; Müller, Ulrich; Kachar, Bechara (2007). "Cadherin 23 and protocadherin 15 interact to form tip-link filaments in sensory hair cells". Nature. 449 (7158): 87–91. doi:10.1038/nature06091. PMID 17805295. 
  9. ^ http://www.pnas.org/content/115/4/E676.short

Further reading

External links


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.

Extracellular Cadherin domain Provide feedback

This is an extracellular cadherin (EC) domain which can be found at the N-terminal region of Protocadherin 15 (Pcdh15). Pcdh15 features exceptionally long extracellular domains containing 11 ECs [1]. These repeats are structurally similar, but not identical in sequence, often featuring linkers with conserved calcium-binding sites that confer mechanical strength to them [2].

Literature references

  1. Sotomayor M, Weihofen WA, Gaudet R, Corey DP;, Nature. 2012;492:128-132.: Structure of a force-conveying cadherin bond essential for inner-ear mechanotransduction. PUBMED:23135401 EPMC:23135401

  2. Powers RE, Gaudet R, Sotomayor M;, Structure. 2017;25:482-495.: A Partial Calcium-Free Linker Confers Flexibility to Inner-Ear Protocadherin-15. PUBMED:28238533 EPMC:28238533


This tab holds annotation information from the InterPro database.

No InterPro data for this Pfam family.

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 E-set (CL0159), which has the following description:

This clan includes a diverse range of domains that have an Ig-like fold and appear to be distantly related to each other. The clan includes: PKD domains, cadherins and several families of bacterial Ig-like domains as well as viral tail fibre proteins. it also includes several Fibronectin type III domain-containing families.

The clan contains the following 218 members:

A2M A2M_BRD A2M_recep Adeno_GP19K AlcCBM31 Alpha-amylase_N Alpha_adaptinC2 Alpha_E2_glycop Arch_flagellin Arylsulfotran_N ASF1_hist_chap ATG19_autophagy BACON Big_1 Big_10 Big_11 Big_2 Big_3 Big_3_2 Big_3_3 Big_3_5 Big_4 Big_5 Big_6 Big_7 Big_8 Big_9 Bile_Hydr_Trans BiPBP_C bMG1 bMG10 bMG3 bMG5 bMG6 BslA BsuPI Cadherin Cadherin-like Cadherin_2 Cadherin_3 Cadherin_4 Cadherin_5 Cadherin_pro CagX Calx-beta Candida_ALS_N CARDB CBM39 CBM_X2 CD45 CelD_N Ceramidse_alk_C CHB_HEX_C CHB_HEX_C_1 ChitinaseA_N ChiW_Ig_like CHU_C Coatamer_beta_C COP-gamma_platf CopC Cyc-maltodext_N Cytomega_US3 DsbC DUF11 DUF1410 DUF1425 DUF1929 DUF2271 DUF3244 DUF3327 DUF3416 DUF3458 DUF3501 DUF3823_C DUF3859 DUF3872 DUF4165 DUF4179 DUF4426 DUF4448 DUF4469 DUF4625 DUF4879 DUF4981 DUF4982 DUF5001 DUF5008 DUF5011 DUF5065 DUF5115 DUF525 DUF5643 DUF916 EB_dh ECD EpoR_lig-bind ERAP1_C EstA_Ig_like Filamin FixG_C Flavi_glycop_C FlgD_ig fn3 Fn3-like fn3_2 fn3_4 fn3_5 fn3_6 FN3_7 Fn3_assoc fn3_PAP GBS_Bsp-like Glucodextran_B Glyco_hydro2_C5 Glyco_hydro_2 Glyco_hydro_61 Gmad2 GMP_PDE_delta GPI-anchored Hanta_G1 He_PIG He_PIG_assoc HECW_N HemeBinding_Shp Hemocyanin_C Herpes_BLLF1 HYR IFNGR1 Ig_GlcNase Ig_mannosidase IL12p40_C Il13Ra_Ig IL17R_fnIII_D1 IL17R_fnIII_D2 IL2RB_N1 IL3Ra_N IL4Ra_N IL6Ra-bind Inhibitor_I42 Inhibitor_I71 Integrin_alpha2 Interfer-bind Invasin_D3 IRK_C IrmA Iron_transport LEA_2 Lep_receptor_Ig LIFR_N Lipase_bact_N LPMO_10 LRR_adjacent LTD Mannosidase_ig MG1 MG2 MG3 MG4 Mo-co_dimer N_BRCA1_IG Na_K-ATPase NEAT Neocarzinostat Neurexophilin NPCBM_assoc PapD_C PBP-Tp47_c Peptidase_C25_C Phlebovirus_G2 PhoD_N PKD PKD_2 PKD_3 Pollen_allerg_1 Pox_vIL-18BP Pur_ac_phosph_N Qn_am_d_aII Qn_am_d_aIII RabGGT_insert Reeler REJ RET_CLD1 RET_CLD3 RET_CLD4 RGI_lyase RHD_dimer Rho_GDI Rib SCAB-Ig SKICH SLAM SoxZ SprB SusE SVA SWM_repeat T2SS-T3SS_pil_N Tafi-CsgC TarS_C1 TcA_RBD TcfC TIG TIG_2 TIG_plexin Tissue_fac Top6b_C Transglut_C Transglut_N TRAP_beta Tuberculin UL16 Velvet WIF Wzt_C Y_Y_Y YBD ZirS_C Zona_pellucida

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, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...

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Full
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(1119)
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RP15
(12)
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(50)
RP55
(101)
RP75
(166)
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(4)
Full
(275)
Representative proteomes UniProt
(447)
NCBI
(1119)
Meta
(0)
RP15
(12)
RP35
(50)
RP55
(101)
RP75
(166)
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  Seed
(4)
Full
(275)
Representative proteomes UniProt
(447)
NCBI
(1119)
Meta
(0)
RP15
(12)
RP35
(50)
RP55
(101)
RP75
(166)
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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

This family is new in this Pfam release.

Seed source: ECOD:EUF04679
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: El-Gebali S
Number in seed: 4
Number in full: 275
Average length of the domain: 101.60 aa
Average identity of full alignment: 82 %
Average coverage of the sequence by the domain: 6.11 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.0 25.0
Trusted cut-off 40.0 38.7
Noise cut-off 22.9 19.7
Model length: 110
Family (HMM) version: 1
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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Tree controls

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The tree shows the occurrence of this domain across different species. More...

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Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

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 ECD domain has been found. There are 8 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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