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786  structures 929  species 0  interactions 278836  sequences 2360  architectures

Family: Cadherin (PF00028)

Summary: Cadherin domain

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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 the membrane through vinculin. The head domain of vinculin is associated with 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 are important in the formation of adherens junctions to allow cells to adhere to each other .[1] Cadherins are a class of type-1 transmembrane proteins, and 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 numerous adaptors and signaling proteins, collectively referred to as the cadherin adhesome.

The cadherin family is essential in maintaining the cell-cell contact and regulating cytoskeletal complexes. The cadherin superfamily includes cadherins, protocadherins, desmogleins, desmocollins, and more.[2][3] In structure, they share cadherin repeats, which are the extracellular Ca2+-binding domains. There are multiple classes of cadherin molecules, each designated with a prefix (in general, noting the types of tissue with which it is associated). Classical cadherins maintain the tone of tissues by forming a homodimer in cis while desmosomal cadherins are heterodimeric.[4] The intracellular portion of classical cadherins interacts with a complex of proteins that allows connection to the actin cytoskeleton. Although classical cadherins take a role in cell layer formation and structure formation, desmosomal cadherins focus on resisting cell damage. Desmosomal cadherins are responsible to maintain the function of desmosomes that is to overturn the mechanical stress of the tissues. Similar to classical cadherins, desmosomal cadherins has a single transmembrane domain, five EC repeats, and an intracellular domain. Two types of desmosomal cadherins exist, and they are called desmogleins and desmocollins that contains an intracellular anchor and cadherin like sequence (ICS). The adaptor proteins that associate with desmosomal cadherins are plakoglobin (related to -catenin), plakophilins (p120 catenin subfamily), and desmoplakins. The major function of desmoplakins to bind to intermediate filament thorough interaction with plakoglobin that attaches to ICS of desmogleins and desmocollins and plakophilins. A[4] typical cadherins are different from other types of cadherins and consist of one or more extracellular repeat domains. The components that build an atypical cadherin are flamingo (seven pass transmembrane) and Dcad102F-like cadherins. Their job is to take part in signaling pathway instead of performing cell-cell adhesion.

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.[5] 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.[6] In addition, several groups have observed heterotypic binding affinity (i.e., binding of different types of cadherin together) in various assays.[7][8] 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.[9]

Structure

Domain organization of different types of cadherins

Cadherins are synthesized as polypeptides and undergo many post-translational modifications to become the proteins which mediate cell-cell adhesion and recognition.[10] These polypeptides are approximately 720–750 amino acids long. Each cadherin has a small C-terminal 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.[11]  Because cadherins are Ca2+ dependent, they have five tandem extracellular domain repeats that act as the binding site for Ca2+ ions.[12]  Their extracellular domain interacts with two separate trans dimer conformations: strand-swap dimers (S-dimers) and X-dimers.[12] To date, over 100 types of cadherins in humans have been identified and sequenced.[13]

 The functionality of cadherins relies upon the formation of two identical subunits, known as homodimers.[11] 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.[11] 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 cytoplasmic portion of the cadherin.[11] Regulatory proteins include p-120 catenin, -catenin,  -catenin, and vinculin. Binding of p-120 catenin and -catenin to the homodimer increases the stability of the classical cadherin. -catenin is engaged by p120-catenin complex, where vinculin is recruited to take a role in indirect association with actin cytoskeleton.[4] However, cadherin-catenin complex can also bind directly to the actin without the help of vinculin. Moreover, the strength of cadherin adhesion can increase by dephosphorylation of p120 catenin and the binding of -catenin and vinculin.

Function

Development

Cadherins behave as both receptors and ligands for other molecules. During development, their behavior assists at properly positioning cells: they are responsible for the separation of the different tissue layers and for cellular migration.[14] In the very early stages of development, E-cadherins (epithelial cadherin) are 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 a neural plate forms in an embryo, the tissues residing near the cranial neural folds have decreased N-cadherin expression.[15] Conversely, the expression of the N-cadherins remains unchanged in other regions of the neural tube that is located on the anterior-posterior axis of the vertebrate.[15] N-cadherins have different functions that maintain the cell structure, cell-cell adhesion, internal adhesions. They participate greatly in keeping the ability of the structured heart due to pumping and release blood. Because of the contribution of N-cadherins adhering strongly between the cardiomyocytes, the heart can overcome the fracture, deformation, and fatigue that can result from the blood pressure.[16] N-cadherin takes part in the development of the heart during embryo, especially in sorting out of the precardiac mesoderm. N-cadherins are robustly expressed in precardiac mesoderm, but they do not take a role in cardiac linage. An embryo with N-cadherin mutation still forms the primitive heart tube; however, N-cadherin deficient mice will have difficulties in maintaining the cardiomyocytes development.[16] The myocytes of these mice will end up with dissociated myocytes surrounding the endocardial cell layer when they cannot preserve the cell adhesion due to the heart starting to pump. As a result, the cardiac outflow tract will be blocked causing cardiac swelling.The expression of different types of cadherins in the cells varies dependent upon the specific differentiation and specification of an organism during development. Cadherins play a vital role in the migration of cells through the epithelial-mesenchymal transition (EMT), which requires cadherins to form 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.[15] In addition, cadherins that are 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.[13] Regulation of cadherin expression can occur through promoter methylation among other epigenetic mechanisms.[17]

Tumour metastasis

The E-cadherin–catenin complex plays a key role in cellular adhesion; loss of this function has been associated with increased invasiveness and metastasis of tumors.[18] The suppression of E-cadherin expression is regarded as one of the main molecular events responsible for dysfunction in cell-cell adhesion, which can lead to local invasion and ultimately tumor development. Because E-cadherins play an important role in tumor suppression, they are also referred to as the "suppressors of invasion".[19]

Correlation to cancer

It has been discovered that cadherins and other additional factors are correlated to the formation and growth of some cancers and how a tumor continues to grow. The E-cadherins, known as the epithelial cadherins, are on the surface of one cell and can bind with those of the same kind on another to form bridges.[20] The loss of the cell adhesion molecules, E cadherins, is causally involved in the formation of epithelial types of cancers such as carcinomas. The changes in any types of cadherin expression may not only control tumor cell adhesion but also may affect signal transduction leading to the cancer cells growing uncontrollably.[21]

In epithelial cell cancers, disrupted cell to cell adhesion might lead to the development of secondary malignant growths; they are distant from the primary site of cancer and can result from the abnormalities in the expression of E-cadherins or its associated catenins. CAMs such as the cadherin glycoproteins that normally function as the glue and holds cells together act as important mediators of cell to cell interactions. E-cadherins, on the surface of all epithelial cells, are linked to the actin cytoskeleton through interactions with catenins in the cytoplasm. Thus, anchored to the cytoskeleton, E-cadherins on the surface of one cell can bind with those on another to form bridges. In epithelial cell cancers, disrupted cell-cell adhesion that might lead to metastases can result from abnormalities in the expression of E-cadherin or its associated catenins.[20]

Correlation to endometrium and embryogenesis

This family of glycoproteins is responsible for calcium-dependent mechanism of intracellular adhesion. E-cadherins are crucial in embryogenesis during several processes, including gastrulation, neurulation, and organogenesis. Furthermore, suppression of E-cadherins impairs intracellular adhesion. The levels of these molecules increase during the luteal phase while their expression is regulated by progesterone with endometrial calcitonin.[22]

Types

Cadherin domain (repeat)
ECadherin repeating unit.png
Ribbon representation of a repeating unit in the extracellular E-cadherin ectodomain of the mouse (PDB: 3Q2V​) [23]
Identifiers
SymbolCadherin
PfamPF00028
InterProIPR002126
SMARTCA
PROSITEPDOC00205
SCOP21nci / SCOPe / SUPFAM
Membranome114
See Pfam CL0159 for other Cadherin families.

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.[24][25] These large amount of diversities are accomplished by having multiple cadherin encoding genes combined with alternative RNA splicing mechanisms. Invertebrates contain fewer than 20 types of cadherins.[25]

Classical

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

  • CDH1 – E-cadherin (epithelial): E-cadherins are found in epithelial tissue; not to be confused with the APC/C activator protein CDH1.
  • 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

Protocadherins are the largest mammalian subgroup of the cadherin superfamily of homophilic cell-adhesion proteins.

Unconventional/ungrouped

See also

References

  1. ^ a b Alimperti S, Andreadis ST (May 2015). "CDH2 and CDH11 act as regulators of stem cell fate decisions". Stem Cell Research. 14 (3): 270–82. doi:10.1016/j.scr.2015.02.002. PMC 4439315. PMID 25771201.
  2. ^ Hulpiau P, van Roy F (February 2009). "Molecular evolution of the cadherin superfamily". The International Journal of Biochemistry & Cell Biology. 41 (2): 349–69. doi:10.1016/j.biocel.2008.09.027. PMID 18848899.
  3. ^ Angst BD, Marcozzi C, Magee AI (February 2001). "The cadherin superfamily: diversity in form and function". Journal of Cell Science. 114 (Pt 4): 629–41. doi:10.1242/jcs.114.4.629. PMID 11171368.
  4. ^ a b c Priest AV, Koirala R, Sivasankar S (December 2019). "Single-molecule studies of classical and desmosomal cadherin adhesion". Current Opinion in Biomedical Engineering. 12: 43–50. doi:10.1016/j.cobme.2019.08.006. PMC 6859941. PMID 31742239.
  5. ^ Bello SM, Millo H, Rajebhosale M, Price SR (January 2012). "Catenin-dependent cadherin function drives divisional segregation of spinal motor neurons". The Journal of Neuroscience. 32 (2): 490–505. doi:10.1523/jneurosci.4382-11.2012. PMC 3292792. PMID 22238085.
  6. ^ Duguay D, Foty RA, Steinberg MS (January 2003). "Cadherin-mediated cell adhesion and tissue segregation: qualitative and quantitative determinants". Developmental Biology. 253 (2): 309–23. doi:10.1016/S0012-1606(02)00016-7. PMID 12645933.
  7. ^ Niessen CM, Gumbiner BM (January 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 2199232. PMID 11790800.
  8. ^ Volk T, Cohen O, Geiger B (September 1987). "Formation of heterotypic adherens-type junctions between L-CAM-containing liver cells and A-CAM-containing lens cells". Cell. 50 (6): 987–94. doi:10.1016/0092-8674(87)90525-3. PMID 3621349. S2CID 21428349.
  9. ^ Bayas MV, Leung A, Evans E, Leckband D (February 2006). "Lifetime measurements reveal kinetic differences between homophilic cadherin bonds". Biophysical Journal. 90 (4): 1385–95. Bibcode:2006BpJ....90.1385B. doi:10.1529/biophysj.105.069583. PMC 1367289. PMID 16326909.
  10. ^ Harris TJ, Tepass U (July 2010). "Adherens junctions: from molecules to morphogenesis". Nature Reviews. Molecular Cell Biology. 11 (7): 502–14. doi:10.1038/nrm2927. PMID 20571587. S2CID 13638902.
  11. ^ a b c d Marie PJ, Haÿ E, Modrowski D, Revollo L, Mbalaviele G, Civitelli R (January 2014). "Cadherin-mediated cell-cell adhesion and signaling in the skeleton". Calcified Tissue International. 94 (1): 46–54. doi:10.1007/s00223-013-9733-7. PMC 4272239. PMID 23657489.
  12. ^ a b Priest AV, Shafraz O, Sivasankar S (September 2017). "Biophysical basis of cadherin mediated cell-cell adhesion". Experimental Cell Research. 358 (1): 10–13. doi:10.1016/j.yexcr.2017.03.015. PMID 28300566.
  13. ^ a b Tepass U, Truong K, Godt D, Ikura M, Peifer M (November 2000). "Cadherins in embryonic and neural morphogenesis". Nature Reviews. Molecular Cell Biology. 1 (2): 91–100. doi:10.1038/35040042. PMID 11253370. S2CID 1632053.
  14. ^ Gumbiner BM (August 2005). "Regulation of cadherin-mediated adhesion in morphogenesis". Nature Reviews. Molecular Cell Biology. 6 (8): 622–34. doi:10.1038/nrm1699. PMID 16025097. S2CID 25094246.
  15. ^ a b c Taneyhill LA, Schiffmacher AT (June 2017). "Should I stay or should I go? Cadherin function and regulation in the neural crest". Genesis. 55 (6): e23028. doi:10.1002/dvg.23028. PMC 5468476. PMID 28253541.
  16. ^ a b Roy, Frans (2013). The Molecular Biology of Cadherins. Elsevier. pp. 264–274. ISBN 978-0-12-394311-8.
  17. ^ Reinhold WC, Reimers MA, Maunakea AK, Kim S, Lababidi S, Scherf U, et al. (February 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.
  18. ^ 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.
  19. ^ Nives Pećina-Šlaus (2003). "Tumor suppressor gene E-cadherin and its role in normal and malignant cells". Cancer Cell Int. 3 (17): 17. doi:10.1186/1475-2867-3-17. PMC 270068. PMID 14613514.
  20. ^ a b Morales CP, Souza RF, Spechler SJ (November 2002). "Hallmarks of cancer progression in Barrett's oesophagus". Lancet. 360 (9345): 1587–9. doi:10.1016/S0140-6736(02)11569-8. PMID 12443613. S2CID 22401564.
  21. ^ Cavallaro U, Schaffhauser B, Christofori G (February 2002). "Cadherins and the tumour progression: is it all in a switch?". Cancer Letters. 176 (2): 123–8. doi:10.1016/S0304-3835(01)00759-5. PMID 11804738.
  22. ^ Grigorian IY, Linkova NS, Polyakova VO, Paltseva EM, Kozlov KL (January 2016). "Signaling molecules of the endometrium: Gerontological and general pathological aspects". Advances in Gerontology. 6 (1): 36–43. doi:10.1134/S2079057016010045. S2CID 87472683.
  23. ^ Harrison OJ, Jin X, Hong S, Bahna F, Ahlsen G, Brasch J, et al. (February 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 3070544. PMID 21300292.
  24. ^ Offermanns S, Rosenthal W (2008). Encyclopedia of Molecular Pharmacology. Springer. pp. 306–. ISBN 978-3-540-38916-3. Retrieved 14 December 2010.
  25. ^ a b Lodish H, Berk A, Kaiser C, Krieger M, Bretscher A, Ploegh H, Amon A (2013). Molecular Cell Biology (Seventh ed.). New York: Worth Publ. p. 934. ISBN 978-1-4292-3413-9.

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.

Cadherin domain Provide feedback

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Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002126

Cadherins are a group of transmembrane proteins that serve as the major adhesion molecules located within adherens junctions. They can regulate cell-cell adhesion through their extracellular domain and their cytosolic domains connect to the actin cytoskeleton by binding to catenins [ PUBMED:25014356 ]. These proteins preferentially interact with themselves in a homophilic manner in connecting cells; thus acting as both receptor and ligand. They may play an important role in the sorting of different cell types during morphogenesis, histogenesis and regeneration. They may also be involved in the regulation of tight and gap junctions, and in the control of intercellular spacing. Cadherins are evolutionary related to the desmogleins which are component of intercellular desmosome junctions involved in the interaction of plaque proteins.

Structurally, cadherins comprise a number of domains: classically, these include a signal sequence; a propeptide of around 130 residues; a single transmembrane domain and five tandemly repeated extracellular cadherin domains, 4 of which are cadherin repeats, and the fifth contains 4 conserved cysteines and a C-terminal cytoplasmic domain [ PUBMED:11736639 ]. However, proteins are designated as members of the broadly defined cadherin family if they have one or more cadherin repeats. A cadherin repeat is an independently folding sequence of approximately 110 amino acids that contains motifs with the conserved sequences DRE, DXNDNAPXF, and DXD. Crystal structures have revealed that multiple cadherin domains form Ca2+-dependent rod-like structures with a conserved Ca2+-binding pocket at the domain-domain interface. Cadherins depend on calcium for their function: calcium ions bind to specific residues in each cadherin repeat to ensure its proper folding, to confer rigidity upon the extracellular domain and is essential for cadherin adhesive function and for protection against protease digestion.

This entry represents the extracellular repeated domains found in cadherins and related proteins.

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 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 257 members:

A2M A2M_BRD A2M_recep AA9 Adeno_GP19K AlcCBM31 Alpha-amylase_N Alpha_adaptinC2 Alpha_E2_glycop Anth_Ig aRib Arylsulfotran_N ASF1_hist_chap ATG19 BACON BACON_2 BatD BIg21 Big_1 Big_10 Big_11 Big_12 Big_13 Big_14 Big_15 Big_2 Big_3 Big_3_2 Big_3_3 Big_3_4 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 Chlam_OMP6 CHU_C Coatamer_beta_C COP-gamma_platf CopC CshA_repeat Cyc-maltodext_N Cytomega_US3 DBB DsbC DUF11 DUF1410 DUF1425 DUF2271 DUF3244 DUF3458 DUF3501 DUF3823_C DUF3859 DUF4165 DUF4179 DUF4426 DUF4469 DUF4625 DUF4784_N DUF4879 DUF4959 DUF4982 DUF4998 DUF5001 DUF5008 DUF5011 DUF5060 DUF5065 DUF5103 DUF5115 DUF525 DUF5643 DUF6383 DUF6595 DUF916 EB_dh ECD Enterochelin_N EpoR_lig-bind ERAP1_C EstA_Ig_like Expansin_C 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 GlgE_dom_N_S Glucodextran_B Glyco_hydro2_C5 Glyco_hydro_2 Gmad2 GMP_PDE_delta GO-like_E_set GspA_SrpA_N Hanta_G1 He_PIG HECW_N HemeBinding_Shp Hemocyanin_C Herpes_BLLF1 HYR IalB 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 InlK_D3 Integrin_alpha2 Interfer-bind Invasin_D3 IRK_C IrmA Iron_transport Kre9_KNH LacZ_4 LEA_2 Lep_receptor_Ig LIFR_D2 LIFR_N Lipase_bact_N LodA_N LPMO_10 LRR_adjacent LTD MALT1_Ig Mannosidase_ig MetallophosC MG1 MG2 MG3 MG4 Mo-co_dimer N_BRCA1_IG Na_K-ATPase NAR2 NDNF NDNF_C NEAT Neocarzinostat Neurexophilin NPCBM_assoc Omp28 PapD_C PBP-Tp47_c Peptidase_C25_C Phlebo_G2_C PhoD_N PKD PKD_2 PKD_3 PKD_4 PKD_5 PKD_6 Por_Secre_tail Pox_vIL-18BP Psg1 PTP_tm Pullulanase_N2 Pur_ac_phosph_N Qn_am_d_aIII Qn_am_d_aIV RabGGT_insert Reeler REJ RET_CLD1 RET_CLD3 RET_CLD4 RGI_lyase RHD_dimer Rho_GDI Rib RibLong 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 TIG_SUH Tissue_fac Top6b_C TPPII TQ Transglut_C Transglut_N TRAP_beta TraQ_transposon UL16 Velvet WIF Wzt_C Y_Y_Y YBD YscW 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 and the UniProtKB sequence database. More...

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  Seed
(55)
Full
(278836)
Representative proteomes UniProt
(455561)
RP15
(34606)
RP35
(87224)
RP55
(209664)
RP75
(284697)
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  Seed
(55)
Full
(278836)
Representative proteomes UniProt
(455561)
RP15
(34606)
RP35
(87224)
RP55
(209664)
RP75
(284697)
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  Seed
(55)
Full
(278836)
Representative proteomes UniProt
(455561)
RP15
(34606)
RP35
(87224)
RP55
(209664)
RP75
(284697)
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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.

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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: Swissprot_feature_table
Previous IDs: cadherin;
Type: Domain
Sequence Ontology: SO:0000417
Author: Sonnhammer ELL
Number in seed: 55
Number in full: 278836
Average length of the domain: 93.10 aa
Average identity of full alignment: 25 %
Average coverage of the sequence by the domain: 45.26 %

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 28.8 28.8
Trusted cut-off 28.8 28.8
Noise cut-off 28.7 28.7
Model length: 93
Family (HMM) version: 20
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 Cadherin domain has been found. There are 786 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
A0A0A6YY83 View 3D Structure Click here
A0A0B4LHM7 View 3D Structure Click here
A0A0G2K294 View 3D Structure Click here
A0A0G2K6T9 View 3D Structure Click here
A0A0G2K7Z8 View 3D Structure Click here
A0A0G2K8I5 View 3D Structure Click here
A0A0G2K9D7 View 3D Structure Click here
A0A0G2KA90 View 3D Structure Click here
A0A0G2KGN6 View 3D Structure Click here
A0A0G2L110 View 3D Structure Click here
A0A0G2L2D6 View 3D Structure Click here
A0A0G2L2S7 View 3D Structure Click here
A0A0G2L4D7 View 3D Structure Click here
A0A0G2L924 View 3D Structure Click here
A0A0H2UKU4 View 3D Structure Click here
A0A0J9YJK6 View 3D Structure Click here
A0A0N4SU21 View 3D Structure Click here
A0A0N4SUB1 View 3D Structure Click here
A0A0N4SUG2 View 3D Structure Click here
A0A0R4I9J8 View 3D Structure Click here
A0A0R4I9U6 View 3D Structure Click here
A0A0R4I9W0 View 3D Structure Click here
A0A0R4IAV5 View 3D Structure Click here
A0A0R4IAX7 View 3D Structure Click here
A0A0R4IBQ5 View 3D Structure Click here
A0A0R4IEA8 View 3D Structure Click here
A0A0R4IEF6 View 3D Structure Click here
A0A0R4IF36 View 3D Structure Click here
A0A0R4IFD4 View 3D Structure Click here
A0A0R4IFF8 View 3D Structure Click here
A0A0R4IHN2 View 3D Structure Click here
A0A0R4II09 View 3D Structure Click here
A0A0R4IIE9 View 3D Structure Click here
A0A0R4ILP7 View 3D Structure Click here
A0A0R4IM30 View 3D Structure Click here
A0A0R4IM90 View 3D Structure Click here
A0A0R4IML6 View 3D Structure Click here
A0A0R4IMS0 View 3D Structure Click here
A0A0R4IP57 View 3D Structure Click here
A0A0R4IQQ5 View 3D Structure Click here