{"uniprot":"Q9P2V4","gene":"LRIT1","name":"Leucine-rich repeat, immunoglobulin-like domain and transmembrane domain-containing protein 1","organism":"Homo sapiens (Human)","status":"dark","length":623,"sequence":"MRVALGMLWLLALAWPPQARGFCPSQCSCSLHIMGDGSKARTVVCNDPDMTLPPASIPPDTSRLRLERTAIRRVPGEAFRPLGRLEQLWLPYNALSELNALMLRGLRRLRELRLPGNRLAAFPWAALRDAPKLRLLDLQANRLSAVPAEAARFLENLTFLDLSSNQLMRLPQELIVSWAHLETGIFPPGHHPRRVLGLQDNPWACDCRLYDLVHLLDGWAPNLAFIETELRCASPRSLAGVAFSQLELRKCQGPELHPGVASIRSLLGGTALLRCGATGVPGPEMSWRRANGRPLNGTVHQEVSSDGTSWTLLGLPAVSHLDSGDYICQAKNFLGASETVISLIVTEPPTSTEHSGSPGALWARTGGGGEAAAYNNKLVARHVPQIPKPAVLATGPSVPSTKEELTLEHFQMDALGELSDGRAGPSEARMVRSVKVVGDTYHSVSLVWKAPQAKNTTAFSVLYAVFGQHSMRRVIVQPGKTRVTITGLLPKTKYVACVCVQGLVPRKEQCVIFSTNEVVDAENTQQLINVVVISVAIVIALPLTLLVCCSALQKRCRKCFNKDSTEATVTYVNLERLGYSEDGLEELSRHSVSEADRLLSARSSVDFQAFGVKGGRRINEYFC","function_summary":"A single-pass type I membrane glycoprotein with an extensive extracellular leucine-rich repeat scaffold followed by immunoglobulin-like and fibronectin type III modules that collectively create a high-affinity binding platform. By assembling and stabilizing extracellular and membrane-proximal complexes, it modulates signaling pathways, notably tuning fibroblast growth factor receptor outputs. Its maturation and assembly occur prominently in the endoplasmic reticulum membrane, where it folds and organizes into regulatory assemblies that influence receptor trafficking and signal attenuation.","plain_language":"LRIT1 has barely been studied. The model's best guess: A single-pass type I membrane glycoprotein with an extensive extracellular leucine-rich repeat scaffold followed by immunoglobulin-like and fibronectin type III modules that collectively create a high-affinity binding platform. By assembling and stabilizing extracellular and membrane-proximal complexes, it modulates signaling pathways, notably tuning fibroblast growth factor receptor outputs.","uniprot_summary":"Possible function in signal transduction.","go_terms":{"molecular_function":[{"id":"GO:0005515","label":"protein binding"}],"biological_process":[{"id":"GO:0040036","label":"regulation of fibroblast growth factor receptor signaling pathway"}],"cellular_component":[{"id":"GO:0016020","label":"membrane"},{"id":"GO:0005789","label":"endoplasmic reticulum membrane"}]},"interpro":[{"id":"IPR032675","name":"Leucine-rich repeat domain superfamily","type":"homologous_superfamily","start":22,"end":253},{"id":"IPR013783","name":"Immunoglobulin-like fold","type":"homologous_superfamily","start":254,"end":358},{"id":"IPR036179","name":"Immunoglobulin-like domain superfamily","type":"homologous_superfamily","start":258,"end":351},{"id":"IPR013783","name":"Immunoglobulin-like fold","type":"homologous_superfamily","start":425,"end":515},{"id":"IPR036116","name":"Fibronectin type III superfamily","type":"homologous_superfamily","start":431,"end":500},{"id":"IPR000483","name":"Cysteine-rich flanking region, C-terminal","type":"domain","start":201,"end":252},{"id":"IPR007110","name":"Immunoglobulin-like domain","type":"domain","start":254,"end":346},{"id":"IPR003599","name":"Immunoglobulin domain subtype","type":"domain","start":260,"end":346},{"id":"IPR003598","name":"Immunoglobulin subtype 2","type":"domain","start":266,"end":335},{"id":"IPR013098","name":"Immunoglobulin I-set","type":"domain","start":267,"end":345},{"id":"IPR003961","name":"Fibronectin type III","type":"domain","start":430,"end":518},{"id":"IPR050467","name":"Leucine-rich repeat and fibronectin type-III domain-containing","type":"family","start":13,"end":558},{"id":"IPR003591","name":"Leucine-rich repeat, typical subtype","type":"repeat","start":82,"end":105},{"id":"IPR003591","name":"Leucine-rich repeat, typical subtype","type":"repeat","start":106,"end":129},{"id":"IPR001611","name":"Leucine-rich repeat","type":"repeat","start":107,"end":177},{"id":"IPR003591","name":"Leucine-rich repeat, typical subtype","type":"repeat","start":131,"end":153},{"id":"IPR003591","name":"Leucine-rich repeat, typical subtype","type":"repeat","start":154,"end":177}],"reasoning":"I begin by dissecting the domain architecture. The N-terminal half is dominated by IPR032675 (Leucine-rich repeat domain superfamily, residues 22–253), which is reinforced by multiple LRR repeat calls: IPR003591 typical LRRs at positions 82–105, 106–129, 131–153, and 154–177, together forming a curved solenoid scaffold specialized for avid, shape-complementary protein binding. Immediately C-terminal to the LRR stack sits IPR000483 (Cysteine-rich flanking region, C-terminal, residues 201–252), a hallmark cap that stabilizes LRR termini and constrains ligand-binding geometry. Following this, the ectodomain transitions into immunoglobulin-like modules: IPR013783 (Immunoglobulin-like fold, residues 254–358) and its superfamily IPR036179 (Immunoglobulin-like domain superfamily, residues 258–351), with more specific Ig annotations IPR007110 (Immunoglobulin-like domain, residues 254–346), IPR003599 (Immunoglobulin domain subtype, residues 260–346), IPR003598 (Immunoglobulin subtype 2, residues 266–335), and IPR013098 (Immunoglobulin I-set, residues 267–345). This Ig block provides rigid β-sandwich surfaces that extend and tune the binding interface of the LRR platform. Distally, a second Ig-like region is annotated by IPR013783 (Immunoglobulin-like fold, residues 425–515), followed by IPR036116 (Fibronectin type III superfamily, residues 431–500) and a concrete IPR003961 (Fibronectin type III, residues 430–518). FNIII modules often follow Ig domains in extracellular adhesion and signaling receptors, acting as spacer and auxiliary ligand-binding surfaces. The overall architecture—LRR core capped by Ig and FNIII modules—is diagnostic of the IPR050467 family (Leucine-rich repeat and fibronectin type-III domain-containing, residues 13–558), a class of single-pass type I membrane proteins that mediate extracellular protein–protein interactions.\n\nThis ordered ectodomain, together with a single-pass type I topology, dictates molecular function. The LRR solenoid and Ig/FNIII tandem create a high-affinity, multivalent binding platform that captures extracellular or membrane-proximal partners; this causally establishes GO:0005515 protein binding as the operative molecular function. The absence of catalytic motifs and the presence of multiple ligand-binding superfamilies argue for a non-enzymatic, scaffolding role.\n\nFrom this binding-centric function, I infer the biological process. LRR–Ig/FNIII receptors frequently modulate receptor tyrosine kinase pathways by altering receptor clustering, ligand availability, or endocytic routing. The specific process label aligns with this mechanism: GO:0040036 regulation of fibroblast growth factor receptor signaling pathway. The architecture enables regulation by sequestering or presenting growth factor cues and by influencing receptor trafficking and signal amplitude.\n\nCellular localization follows from topology and maturation. The protein is a single-pass type I membrane protein with a large luminal/extracellular ectodomain and a short cytosolic tail. Such proteins are synthesized and folded in the secretory pathway; the presence of an extensive luminal ectodomain and the annotation of ER residency support GO:0005789 endoplasmic reticulum membrane as a key steady-state or assembly locale. The single-pass architecture and trafficking behavior justify assignment to GO:0016020 membrane, with the ER membrane as a defined site where folding, assembly, and potential quality control occur before delivery to later destinations.\n\nMechanistically, the LRR array nucleates a curved binding surface that captures extracellular ligands or membrane-proximal partners and thereby modulates FGFR pathway flux. The Ig and FNIII modules likely stabilize higher-order assemblies and tune avidity. I hypothesize that this receptor-like molecule tempers FGFR signaling by two coupled routes: (1) altering ligand presentation or sequestration at the cell surface; and (2) controlling receptor and complex endocytosis and recycling via ER/Golgi–proximal checkpoints that bias signaling toward attenuation. Likely interaction partners include FGFRs and their accessory factors, ER chaperones that shepherd folding and assembly, and endocytic adaptors that route complexes toward downregulation. Together, the LRR–Ig/FNIII architecture causes a binding-driven regulatory mechanism that modulates FGF receptor pathway output from an ER-enriched membrane platform.","category":"dark","control_evaluation":null,"validation_plan":null,"structure":{"source":"AlphaFold DB","pdb":"/structures/AF-Q9P2V4.pdb","alphafold":"https://alphafold.ebi.ac.uk/entry/Q9P2V4"},"links":{"uniprot":"https://www.uniprot.org/uniprotkb/Q9P2V4/entry","atlas":"/p/Q9P2V4"},"provenance":{"model":"BioReason-Pro (ESM3 esm3-sm-open-v1)","source_list":"Pharos Tdark","note":"AI prediction, not experimentally verified"}}