{"uniprot":"Q8N9V2","gene":"TRIML1","name":"Probable E3 ubiquitin-protein ligase TRIML1","organism":"Homo sapiens (Human)","status":"dark","length":468,"sequence":"MSTADLMENLREELTCFICLDYFSSPVTTECGHSFCLVCLLRSWEEHNTPLSCPECWRTLEGPHFQSNERLGRLASIARQLRSQVLQSEDEQGSYGRMPTTAKALSDDEQGGSAFVAQSHGANRVHLSSEAEEHHREKLQEILNLLRVRRKEAQAVLTHEKERVKLCQEETKTCKQVVVSEYMKMHQFLKEEEQLQLQLLEQEEKENMRKLRNNEIKLTQQIRSLSKMIAQIESSSQSSAFESLEEVRGALERSEPLLLQCPEATTTELSLCRITGMKEMLRKFSTEITLDPATANAYLVLSEDLKSVKYGGSRQQLPDNPERFDQSATVLGTQIFTSGRHYWEVEVGNKTEWEVGICKDSVSRKGNLPKPPGDLFSLIGLKIGDDYSLWVSSPLKGQHVREPVCKVGVFLDYESGHIAFYNGTDESLIYSFPQASFQEALRPIFSPCLPNEGTNTDPLTICSLNSHV","function_summary":"A cytosolic RING–SPRY scaffold that couples ubiquitin transfer to selective substrate recognition to coordinate antiviral defense and cytoskeletal control. Its N-terminal catalytic module installs mono- and K63-linked ubiquitin marks, while the C-terminal SPRY platform recruits innate immune and cytoskeletal targets. By tuning the stability and interaction states of signaling and structural proteins, it modulates interferon pathways, restrains viral transcription and release, promotes autophagy, and influences cell-cycle progression and transcriptional regulation within the cytoplasm.","plain_language":"TRIML1 has barely been studied. The model's best guess: A cytosolic RING–SPRY scaffold that couples ubiquitin transfer to selective substrate recognition to coordinate antiviral defense and cytoskeletal control. Its N-terminal catalytic module installs mono- and K63-linked ubiquitin marks, while the C-terminal SPRY platform recruits innate immune and cytoskeletal targets.","uniprot_summary":"May be involved in cytoskeletal function.","go_terms":{"molecular_function":[{"id":"GO:0005515","label":"protein binding"}],"biological_process":[{"id":"GO:0031647","label":"regulation of protein stability"},{"id":"GO:0045087","label":"innate immune response"},{"id":"GO:0045787","label":"positive regulation of cell cycle"},{"id":"GO:0032897","label":"negative regulation of viral transcription"},{"id":"GO:0050777","label":"negative regulation of immune response"},{"id":"GO:0045824","label":"negative regulation of innate immune response"},{"id":"GO:0051607","label":"defense response to virus"},{"id":"GO:0032479","label":"regulation of type I interferon production"},{"id":"GO:0043393","label":"regulation of protein binding"},{"id":"GO:0010508","label":"positive regulation of autophagy"},{"id":"GO:0034341","label":"response to type II interferon"},{"id":"GO:0031648","label":"protein destabilization"},{"id":"GO:0051091","label":"positive regulation of DNA-binding transcription factor activity"},{"id":"GO:0032092","label":"positive regulation of protein binding"},{"id":"GO:0044790","label":"suppression of viral release by host"},{"id":"GO:0032088","label":"negative regulation of NF-kappaB transcription factor activity"},{"id":"GO:0051099","label":"positive regulation of DNA-binding transcription factor activity"},{"id":"GO:0051865","label":"protein autoubiquitination"},{"id":"GO:0032868","label":"regulation of NFAT signaling pathway"},{"id":"GO:0006513","label":"protein monoubiquitination"},{"id":"GO:0070534","label":"protein K63-linked ubiquitination"}],"cellular_component":[{"id":"GO:0005829","label":"cytosol"}]},"interpro":[{"id":"IPR013083","name":"Zinc finger, RING/FYVE/PHD-type","type":"homologous_superfamily","start":1,"end":97},{"id":"IPR013320","name":"Concanavalin A-like lectin/glucanase domain superfamily","type":"homologous_superfamily","start":277,"end":464},{"id":"IPR043136","name":"B30.2/SPRY domain superfamily","type":"homologous_superfamily","start":279,"end":468},{"id":"IPR001841","name":"Zinc finger, RING-type","type":"domain","start":16,"end":56},{"id":"IPR001870","name":"B30.2/SPRY domain","type":"domain","start":267,"end":468},{"id":"IPR003879","name":"Butyrophylin-like, SPRY domain","type":"domain","start":284,"end":301},{"id":"IPR006574","name":"SPRY-associated","type":"domain","start":285,"end":337},{"id":"IPR003879","name":"Butyrophylin-like, SPRY domain","type":"domain","start":301,"end":318},{"id":"IPR003879","name":"Butyrophylin-like, SPRY domain","type":"domain","start":323,"end":347},{"id":"IPR003877","name":"SPRY domain","type":"domain","start":338,"end":465},{"id":"IPR003879","name":"Butyrophylin-like, SPRY domain","type":"domain","start":353,"end":366},{"id":"IPR003879","name":"Butyrophylin-like, SPRY domain","type":"domain","start":398,"end":422},{"id":"IPR003879","name":"Butyrophylin-like, SPRY domain","type":"domain","start":429,"end":447},{"id":"IPR050143","name":"Tripartite motif-containing","type":"family","start":11,"end":462},{"id":"IPR017907","name":"Zinc finger, RING-type, conserved site","type":"conserved_site","start":31,"end":40}],"reasoning":"I begin by dissecting the domain architecture. The N-terminus (residues 1–97) is covered by IPR013083 (Zinc finger, RING/FYVE/PHD-type homologous superfamily), with a catalytic core defined by IPR001841 (Zinc finger, RING-type domain, residues 16–56) and its catalytic hallmark reinforced by IPR017907 (Zinc finger, RING-type, conserved site, residues 31–40). This RING module is embedded within IPR050143 (Tripartite motif-containing family, residues 11–462), which characterizes TRIM proteins that use an N-terminal RING to catalyze ubiquitin transfer and often oligomerize via coiled-coils. The C-terminal half is dominated by a SPRY/B30.2 recognition platform: IPR001870 (B30.2/SPRY domain, residues 267–468) and IPR043136 (B30.2/SPRY domain superfamily, residues 279–468) define the overall fold; multiple overlapping butyrophylin-like SPRY annotations (IPR003879, residues 284–301, 301–318, 323–347, 353–366, 398–422, 429–447) and IPR003877 (SPRY domain, residues 338–465) map a modular β-sandwich that confers high-specificity protein binding. IPR006574 (SPRY-associated, residues 285–337) bridges the RING-to-SPRY junction and often stabilizes substrate docking. A broader IPR013320 (Concanavalin A-like lectin/glucanase domain superfamily, residues 277–464) captures the β-sandwich topology shared by SPRY/B30.2 domains rather than carbohydrate hydrolysis. The ordered layout—RING at the N-terminus followed by an extended SPRY platform—creates a two-module machine: the RING executes ubiquitin transfer while the SPRY domain selects and organizes substrates and cofactors.\n\nThis architecture causes a primary molecular function of multivalent protein binding (GO:0005515). The RING domain supplies catalytic potential for ubiquitination, while the SPRY/B30.2 platform provides avid, selective binding surfaces that recruit signaling factors and cytoskeletal regulators. Together, they enable both monoubiquitination and K63-linked polyubiquitin assembly on bound targets.\n\nFrom this molecular function, the biological processes follow. The RING-driven ubiquitin chemistry explains protein monoubiquitination (GO:0006513) and K63-linked ubiquitination (GO:0070534), and supports protein autoubiquitination (GO:0051865). By decorating substrates and adaptors, the protein modulates their stability and interactions, accounting for regulation of protein stability (GO:0031647), protein destabilization (GO:0031648), and positive regulation of protein binding (GO:0032092). The SPRY platform’s affinity for innate immune adaptors and transcriptional regulators positions the protein within the innate immune response (GO:0045087) and defense response to virus (GO:0051607). Its ability to assemble K63 chains and scaffold signaling complexes provides a mechanistic route to negative regulation of viral transcription (GO:0032897) and suppression of viral release by host (GO:0044790). By tuning interferon pathways—through ubiquitin-dependent control of adaptor and transcription factor availability—it participates in regulation of type I interferon production (GO:0032479) and response to type II interferon (GO:0034341). The same ubiquitin-centric control of transcriptional regulators and signaling nodes explains negative regulation of NF-kappaB transcription factor activity (GO:0032088) and bidirectional control of DNA-binding transcription factor activity (GO:0051099 and GO:0051091). Autophagy linkage arises because ubiquitin signaling and SPRY-mediated scaffolding promote selective autophagic pathways, supporting positive regulation of autophagy (GO:0010508). Finally, by stabilizing or removing cell-cycle regulators and autophagy machinery, the protein contributes to positive regulation of cell cycle (GO:0045787).\n\nCellular localization is dictated by the soluble, modular architecture and absence of transmembrane segments. TRIM-family RING–SPRY assemblies typically operate in the cytosol, consistent with GO:0005829 cytosol and the broader cytoplasmic assignment. This soluble environment allows rapid assembly and disassembly of signaling and cytoskeletal complexes.\n\nMechanistically, the N-terminal RING catalyzes ubiquitin transfer while the C-terminal SPRY platform selects substrates and adaptors. This causes selective monoubiquitination or K63-linked polyubiquitination that tunes the abundance and interaction states of innate immune and cytoskeletal factors. I hypothesize that the protein binds and modifies cytosolic targets that govern antiviral defense and cytoskeleton dynamics. Likely partners include cytoskeletal and adhesion regulators (e.g., filamin A and cortactin) that the SPRY domain can capture; innate immune adaptors and transcription factors that route interferon and NF-kappaB signaling; and autophagy machinery that couples ubiquitin signals to vesicular sequestration. Through these assemblies, the protein orchestrates ubiquitin-dependent checkpoints that balance antiviral responses with cytoskeletal remodeling and cell-cycle progression.","category":"dark","control_evaluation":null,"validation_plan":null,"structure":{"source":"AlphaFold DB","pdb":"/structures/AF-Q8N9V2.pdb","alphafold":"https://alphafold.ebi.ac.uk/entry/Q8N9V2"},"links":{"uniprot":"https://www.uniprot.org/uniprotkb/Q8N9V2/entry","atlas":"/p/Q8N9V2"},"provenance":{"model":"BioReason-Pro (ESM3 esm3-sm-open-v1)","source_list":"Pharos Tdark","note":"AI prediction, not experimentally verified"}}