Summary: Extracellular Cadherin domain
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This is the Wikipedia entry entitled "Cadherin". More...
Cadherin Edit Wikipedia article
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This is the Wikipedia entry entitled "PCDH15". More...
PCDH15 Edit Wikipedia article
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
- ^ a b c GRCh38: Ensembl release 89: ENSG00000150275 - Ensembl, May 2017
- ^ a b c GRCm38: Ensembl release 89: ENSMUSG00000052613 - Ensembl, May 2017
- ^ "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
- ^ "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
- ^ 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 1226045. PMID 11398101.
- ^ 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.
- ^ a b c "Entrez Gene: PCDH15 protocadherin 15".
- ^ 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.
- ^ http://www.pnas.org/content/115/4/E676.short
Further reading
- Alagramam KN, Murcia CL, Kwon HY, et al. (2001). "The mouse Ames waltzer hearing-loss mutant is caused by mutation of Pcdh15, a novel protocadherin gene". Nat. Genet. 27 (1): 99–102. doi:10.1038/83837. PMID 11138007.
- Alagramam KN, Yuan H, Kuehn MH, et al. (2001). "Mutations in the novel protocadherin PCDH15 cause Usher syndrome type 1F". Hum. Mol. Genet. 10 (16): 1709–18. doi:10.1093/hmg/10.16.1709. PMID 11487575.
- Ben-Yosef T, Ness SL, Madeo AC, et al. (2003). "A mutation of PCDH15 among Ashkenazi Jews with the type 1 Usher syndrome". N. Engl. J. Med. 348 (17): 1664–70. doi:10.1056/NEJMoa021502. PMID 12711741.
- Zheng QY, Yan D, Ouyang XM, et al. (2005). "Digenic inheritance of deafness caused by mutations in genes encoding cadherin 23 and protocadherin 15 in mice and humans". Hum. Mol. Genet. 14 (1): 103–11. doi:10.1093/hmg/ddi010. PMC 2858222. PMID 15537665.
- Ouyang XM, Yan D, Du LL, et al. (2005). "Characterization of Usher syndrome type I gene mutations in an Usher syndrome patient population". Hum. Genet. 116 (4): 292–9. doi:10.1007/s00439-004-1227-2. PMID 15660226.
- Roux AF, Faugère V, Le Guédard S, et al. (2007). "Survey of the frequency of USH1 gene mutations in a cohort of Usher patients shows the importance of cadherin 23 and protocadherin 15 genes and establishes a detection rate of above 90%". J. Med. Genet. 43 (9): 763–8. doi:10.1136/jmg.2006.041954. PMC 2564578. PMID 16679490.
- Zheng QY, Yu H, Washington JL, et al. (2007). "A new spontaneous mutation in the mouse protocadherin 15 gene". Hear. Res. 219 (1–2): 110–20. doi:10.1016/j.heares.2006.06.010. PMC 2855306. PMID 16887306.
- Le Guédard S, Faugère V, Malcolm S, et al. (2007). "Large genomic rearrangements within the PCDH15 gene are a significant cause of USH1F syndrome". Mol. Vis. 13: 102–7. PMC 2533038. PMID 17277737.
External links
- GeneReviews/NCBI/NIH/UW entry on Usher Syndrome Type I
- PDBe-KB provides an overview of all the structure information available in the PDB for Human Protocadherin-15 (PCDH15)
 | This article on a gene on human chromosome 10 is a stub. You can help Wikipedia by expanding it. |
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
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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
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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.
InterPro entry IPR041149
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 [PUBMED:23135401]. These repeats are structurally similar, but not identical in sequence, often featuring linkers with conserved calcium-binding sites that confer mechanical strength to them [PUBMED:28238533].
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 233 members:
A2M A2M_BRD A2M_recep Adeno_GP19K AlcCBM31 Alpha-amylase_N Alpha_adaptinC2 Alpha_E2_glycop Arch_flagellin aRib Arylsulfotran_N ASF1_hist_chap ATG19_autophagy BACON BACON_2 BatD BIg21 Big_1 Big_10 Big_11 Big_12 Big_13 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 DsbC DUF11 DUF1410 DUF1425 DUF1929 DUF2271 DUF3244 DUF3327 DUF3416 DUF3458 DUF3501 DUF3823_C DUF3859 DUF4165 DUF4179 DUF4426 DUF4469 DUF4625 DUF4879 DUF4959 DUF4981 DUF4982 DUF4998 DUF5001 DUF5008 DUF5011 DUF5065 DUF5115 DUF525 DUF5643 DUF916 EB_dh ECD 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 Glucodextran_B Glyco_hydro2_C5 Glyco_hydro_2 Glyco_hydro_61 Gmad2 GMP_PDE_delta GPI-anchored Hanta_G1 He_PIG 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 InlK_D3 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 MetallophosC 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 Phlebo_G2_C PhoD_N PKD PKD_2 PKD_3 PKD_4 Por_Secre_tail Pox_vIL-18BP Psg1 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 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 Tissue_fac Top6b_C Transglut_C Transglut_N TRAP_beta TraQ_transposon Tuberculin UL16 Velvet WIF Wzt_C Y_Y_Y YBD ZirS_C Zona_pellucidaAlignments
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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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 (1) |
Full (614) |
Representative proteomes | UniProt (873) |
NCBI (1541) |
Meta (0) |
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| RP15 (12) |
RP35 (64) |
RP55 (309) |
RP75 (593) |
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| PP/heatmap | 1 | ||||||||
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
— not available.
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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 (1) |
Full (614) |
Representative proteomes | UniProt (873) |
NCBI (1541) |
Meta (0) |
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|---|---|---|---|---|---|---|---|---|---|
| RP15 (12) |
RP35 (64) |
RP55 (309) |
RP75 (593) |
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| Raw Stockholm | |||||||||
| Gzipped | |||||||||
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
| Seed source: | ECOD:EUF04679 |
| Previous IDs: | none |
| Type: | Domain |
| Sequence Ontology: | SO:0000417 |
| Author: |
El-Gebali S 
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| Number in seed: | 1 |
| Number in full: | 614 |
| Average length of the domain: | 103.30 aa |
| Average identity of full alignment: | 77 % |
| Average coverage of the sequence by the domain: | 6.13 % |
HMM information
| HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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| Model details: |
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| Model length: | 110 | ||||||||||||
| Family (HMM) version: | 2 | ||||||||||||
| Download: | download the raw HMM for this family |
Species distribution
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Colour assignments
Archea
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Eukaryota
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Viruses
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Unclassified
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Viroids
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Unclassified sequence
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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 ECD domain has been found. There are 13 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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