{"uniprot":"Q9Y5H7","gene":"PCDHA5","name":"Protocadherin alpha-5","organism":"Homo sapiens (Human)","status":"dark","length":936,"sequence":"MVYSRRGSLGSRLLLLWLLLAYWKAGSGQLHYSIPEEAKHGTFVGRIAQDLGLELAELVPRLFRVASKGRGDLLEVNLQNGILFVNSRIDREELCRRRAECSIHLEVIVDRPLQVFHVEVAVKDINDNPPRFSRQEQRLFILESRMPDSRFPLEGASDLDIGANAQLRYRLNPNEYFDLDVKTNEEETNFLELVLRKSLDREETQEHRLLVIATDGGKPELTGTVQLLINVLDANDNAPEFDKSIYNVRLLENAPSGTLVIKLNASDADEGINKEIVYFFSNLVLDDVKSKFIINSNTGEIKVNGELDYEDYNSYEINIDAMDKSTFPLSGHCKVVVKLLDVNDNTPEMAITTLFLPVKEDAPLSTVIALISVSDRDSGANGQVTCSLMPHVPFKLVSTFKNYYSLVLDSALDRESVSVYELVVTARDGGSPSLWATASVSVEVADVNDNAPAFAQPQYTVFVKENNPPGCHIFTVSARDADAQENALVSYSLVERRVGERPLSSYVSVHAESGKVYALQPLDHEEVELLQFQVSARDAGVPPLGSNVTLQVFVLDENDNAPALLVPRVGGTGGAVSELVPRSVGAGHVVAKVRAVDPDSGYNAWLSYELQPAPGSARIPFRVGLYTGEISTTRSLDETEAPRHRLLVLVKDHGEPPLTATATVLVSLVESGQAPKASSRASAGAVGPEAALVDVNVYLIIAICAVSSLLVLTLLLYTALRCSAQPTEAVCTRGKPTLLCSSAVGSWSYSQQRRQRVCSGEAPPKTDLMAFSPSLPQGPTSTDNPRQPNPDWRYSASLRAGMHSSVHLEEAGILRAGPGGPDQQWPTVSSATPEPEAGEVSPPVGAGVNSNSWTFKYGPGNPKQSGPGELPDKFIIPGSPAIISIRQEPTNSQIDKSDFITFGKKEETKKKKKKKKGNKTQEKKEKGNSTTDNSDQ","function_summary":"A single-pass cell-surface adhesion receptor that presents a multi-repeat cadherin ectodomain to mediate calcium-stabilized homophilic binding between neighboring human cells. Its extracellular region forms rigid adhesive interfaces that cluster at cell–cell contacts, while the cytoplasmic tail recruits catenins to couple adhesion to the actin cytoskeleton and signaling. Through this adhesive and cytoskeletal coupling, it stabilizes cell–cell junctions and contributes to tissue organization and neural system development at the plasma membrane.","plain_language":"PCDHA5 has barely been studied. The model's best guess: A single-pass cell-surface adhesion receptor that presents a multi-repeat cadherin ectodomain to mediate calcium-stabilized homophilic binding between neighboring human cells. Its extracellular region forms rigid adhesive interfaces that cluster at cell–cell contacts, while the cytoplasmic tail recruits catenins to couple adhesion to the actin cytoskeleton and signaling.","uniprot_summary":"Cadherins are calcium-dependent cell adhesion proteins. They preferentially interact with themselves in a homophilic manner in connecting cells; cadherins may thus contribute to the formation of multicellular aggregates.","go_terms":{"molecular_function":[{"id":"GO:0005515","label":"protein binding"}],"biological_process":[{"id":"GO:0007155","label":"cell adhesion"},{"id":"GO:0007399","label":"nervous system development"}],"cellular_component":[{"id":"GO:0005886","label":"plasma membrane"}]},"interpro":[{"id":"IPR015919","name":"Cadherin-like superfamily","type":"homologous_superfamily","start":29,"end":121},{"id":"IPR015919","name":"Cadherin-like superfamily","type":"homologous_superfamily","start":126,"end":233},{"id":"IPR015919","name":"Cadherin-like superfamily","type":"homologous_superfamily","start":229,"end":446},{"id":"IPR015919","name":"Cadherin-like superfamily","type":"homologous_superfamily","start":442,"end":568},{"id":"IPR015919","name":"Cadherin-like superfamily","type":"homologous_superfamily","start":558,"end":669},{"id":"IPR013164","name":"Cadherin, N-terminal","type":"domain","start":29,"end":110},{"id":"IPR002126","name":"Cadherin-like","type":"domain","start":33,"end":132},{"id":"IPR002126","name":"Cadherin-like","type":"domain","start":154,"end":241},{"id":"IPR002126","name":"Cadherin-like","type":"domain","start":241,"end":349},{"id":"IPR002126","name":"Cadherin-like","type":"domain","start":350,"end":564},{"id":"IPR002126","name":"Cadherin-like","type":"domain","start":580,"end":677},{"id":"IPR031904","name":"Cadherin, C-terminal catenin-binding domain","type":"domain","start":786,"end":919},{"id":"IPR020894","name":"Cadherin conserved site","type":"conserved_site","start":229,"end":239},{"id":"IPR020894","name":"Cadherin conserved site","type":"conserved_site","start":442,"end":452},{"id":"IPR020894","name":"Cadherin conserved site","type":"conserved_site","start":552,"end":562}],"reasoning":"I begin by dissecting the InterPro architecture, which is dominated by tandem cadherin-like modules that define an extracellular adhesive ectodomain followed by a cytoplasmic tail specialized for cytoskeletal coupling. The N-terminal adhesive region is supported by multiple cadherin signatures: IPR013164 (Cadherin, N-terminal, residues 29–110) and IPR002126 (Cadherin-like domain, residues 33–132) establish the first cadherin repeat that nucleates homophilic binding. This is reinforced by a series of cadherin-like blocks—IPR002126 domains at residues 154–241, 241–349, 350–564, and 580–677—arranged in a linear ectodomain that typifies calcium-dependent adhesion. The cadherin-like superfamily coverage across residues 29–121, 126–233, 229–446, 442–568, and 558–669 indicates a multi-repeat extracellular array that confers rigid, calcium-stabilized binding surfaces. Two conserved cadherin sites—IPR020894 (residues 229–239 and 442–452)—and a downstream motif (residues 552–562) mark canonical Ca2+-binding and adhesive interfaces that rigidify the ectodomain and enable strand-swap/homophilic interactions. The cytoplasmic side is defined by IPR031904 (Cadherin, C-terminal catenin-binding domain, residues 786–919), which creates a docking platform for catenins and thereby couples adhesion to the actin cytoskeleton and signaling hubs.\n\nThis domain architecture dictates molecular function. The tandem cadherin repeats and conserved cadherin sites produce a calcium-stiffened adhesive ectodomain that mediates homophilic cell-cell contacts, while the catenin-binding tail recruits intracellular partners. Together, these features cause broad protein-binding capacity consistent with GO:0005515 protein binding: extracellular homophilic adhesion and intracellular catenin engagement both rely on multivalent protein interactions.\n\nFrom this molecular function, the biological processes follow. Homophilic adhesion mediated by cadherin ectodomains is the canonical engine of GO:0007155 cell adhesion, stabilizing epithelial and neuronal contacts. In neural tissues, cadherin-mediated adhesion instructs tissue patterning and synaptic organization, aligning with GO:0007399 nervous system development. The extracellular adhesive array and intracellular catenin linkage together drive adhesive strength and cytoskeletal anchoring that underpin morphogenesis and circuit assembly.\n\nCellular location is implied by the single-pass type I topology and the adhesive ectodomain. The presence of a long extracellular cadherin array and a cytosolic catenin-binding tail places the protein at the cell surface, matching GO:0005886 plasma membrane. The architecture and membrane annotation together indicate a membrane-embedded adhesion receptor whose luminal domain binds neighboring cells and whose cytosolic tail binds catenins.\n\nMechanistically, the protein likely forms trans-dimers with identical ectodomains on adjacent cells, stabilized by bound calcium at the conserved cadherin sites. This trans-adhesion triggers cis-clustering that amplifies adhesive avidity. The cytoplasmic catenin-binding domain recruits α-, β-, and p120-catenins, which tether the complex to filamentous actin and relay signals that tune junction stability and neuronal differentiation. I therefore hypothesize interactions with catenins (CTNNA1/2/3, CTNNB1/2, CTNND1), filamentous actin, and other protocadherin complexes at adherens junctions, collectively coordinating adhesion with cytoskeletal remodeling and neural circuit formation.","category":"dark","control_evaluation":null,"validation_plan":null,"structure":{"source":"AlphaFold DB","pdb":"/structures/AF-Q9Y5H7.pdb","alphafold":"https://alphafold.ebi.ac.uk/entry/Q9Y5H7"},"links":{"uniprot":"https://www.uniprot.org/uniprotkb/Q9Y5H7/entry","atlas":"/p/Q9Y5H7"},"provenance":{"model":"BioReason-Pro (ESM3 esm3-sm-open-v1)","source_list":"Pharos Tdark","note":"AI prediction, not experimentally verified"}}