{"uniprot":"B2RPK0","gene":"HMGB1P1","name":"Putative high mobility group protein B1-like 1","organism":"Homo sapiens (Human)","status":"dark","length":211,"sequence":"MGKGDPKKPRGKMSSYAFFVQTCREEHKKKHSDASVNFSEFSNKCSERWKTMSAKEKGKFEDMAKADKTHYERQMKTYIPPKGETKKKFKDPNAPKRPPSAFFLFCSEYHPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPGEKKAAKLKEKYEKDIAAYQAKGKPEAAKKGVVKAEKSKKKKEEEEDEEDEEDEEEEDEEDEEDDDDE","function_summary":"A tandem HMG-box chromatin architectural protein that bends DNA and binds RNA to assemble and remodel transcriptional complexes in the nucleus, while also moonlighting at the cell surface and in secretory pathways to modulate adhesion and innate immunity. In the nucleus it acts as both coactivator and corepressor, shaping promoter and enhancer structure and coordinating with transcription and DNA-synthesis machineries. Outside the cell it associates with integrins and binds anionic lipids and inflammatory ligands, supporting defense responses to diverse bacteria and signaling through extracellular and membrane-proximal assemblies.","plain_language":"HMGB1P1 has barely been studied. The model's best guess: A tandem HMG-box chromatin architectural protein that bends DNA and binds RNA to assemble and remodel transcriptional complexes in the nucleus, while also moonlighting at the cell surface and in secretory pathways to modulate adhesion and innate immunity. In the nucleus it acts as both coactivator and corepressor, shaping promoter and enhancer structure and coordinating with transcription and DNA-synthesis machineries.","uniprot_summary":"Multifunctional protein with various roles in different cellular compartments.","go_terms":{"molecular_function":[{"id":"GO:0005515","label":"protein binding"},{"id":"GO:0008289","label":"lipid binding"},{"id":"GO:0044877","label":"protein-containing complex binding"},{"id":"GO:0005178","label":"integrin binding"},{"id":"GO:0003713","label":"transcription coactivator activity"},{"id":"GO:0003714","label":"transcription corepressor activity"},{"id":"GO:0001786","label":"phosphatidylserine binding"},{"id":"GO:0001530","label":"lipopolysaccharide binding"},{"id":"GO:0019956","label":"chemokine binding"},{"id":"GO:0003723","label":"RNA binding"},{"id":"GO:0070182","label":"DNA polymerase binding"},{"id":"GO:0003684","label":"damaged DNA binding"},{"id":"GO:0000976","label":"transcription cis-regulatory region binding"},{"id":"GO:0061629","label":"RNA polymerase II-specific DNA-binding transcription factor binding"},{"id":"GO:0008301","label":"DNA binding, bending"}],"biological_process":[{"id":"GO:0050829","label":"defense response to Gram-negative bacterium"},{"id":"GO:0050830","label":"defense response to Gram-positive bacterium"}],"cellular_component":[{"id":"GO:0009986","label":"cell surface"},{"id":"GO:0005615","label":"extracellular space"},{"id":"GO:0005654","label":"nucleoplasm"},{"id":"GO:0017053","label":"transcription repressor complex"},{"id":"GO:0098797","label":"plasma membrane protein complex"},{"id":"GO:0005783","label":"endoplasmic reticulum"},{"id":"GO:0034774","label":"secretory granule lumen"},{"id":"GO:1904813","label":"ficolin-1-rich granule lumen"},{"id":"GO:0000793","label":"condensed chromosome"}]},"interpro":[{"id":"IPR036910","name":"High mobility group box domain superfamily","type":"homologous_superfamily","start":1,"end":81},{"id":"IPR036910","name":"High mobility group box domain superfamily","type":"homologous_superfamily","start":78,"end":166},{"id":"IPR009071","name":"High mobility group box domain","type":"domain","start":6,"end":80},{"id":"IPR009071","name":"High mobility group box domain","type":"domain","start":94,"end":164},{"id":"IPR050342","name":"High Mobility Group Box (HMGB)","type":"family","start":2,"end":206}],"reasoning":"I begin with the InterPro architecture. The polypeptide is dominated by two HMG-box modules arranged in tandem. The N-terminal HMG box is captured by IPR009071 (High mobility group box domain, residues 6–80), and the C-terminal HMG box is captured by IPR009071 again at residues 94–164. These two DNA-bending modules are bracketed by broader superfamily envelopes: IPR036910 (High mobility group box domain superfamily, residues 1–81) at the N-terminus and IPR036910 again at residues 78–166 overlapping the second box, indicating a bipartite HMG-box core. The entire protein falls within IPR050342 (High Mobility Group Box, residues 2–206), confirming a canonical HMGB-family scaffold specialized for high-affinity binding to distorted or non-B-form nucleic acids and for architectural modulation of chromatin. The ordered tandem HMG-box layout causes strong DNA bending and nucleosome engagement, which in turn creates versatile nucleic acid and protein interaction surfaces.\n\nThis tandem HMG-box architecture dictates molecular function. The HMG boxes confer GO:0008301 DNA binding, bending and GO:0000976 transcription cis-regulatory region binding by stabilizing and sharply bending DNA at enhancers and promoters. Their affinity for non-canonical DNA and RNA explains GO:0003684 damaged DNA binding and GO:0003723 RNA binding, respectively. The chromatin-architectural role positions the protein as a bidirectional regulator of transcription—supporting GO:0003713 transcription coactivator activity and GO:0003714 transcription corepressor activity—by remodeling local chromatin and recruiting or displacing transcriptional assemblies. Direct contacts with transcription machinery are consistent with GO:0061629 RNA polymerase II-specific DNA-binding transcription factor binding and GO:0070182 DNA polymerase binding, which together rationalize its role in chromatin-coupled DNA synthesis and repair.\n\nBeyond the nucleus, the same nucleic acid–affinity surfaces and acidic patches enable interactions with diverse extracellular ligands. This explains GO:0005178 integrin binding at the cell surface and GO:0001786 phosphatidylserine binding, which together anchor a moonlighting role in adhesion and apoptosis signaling. The amphipathic, nucleic acid–binding grooves also accommodate microbial and inflammatory ligands, supporting GO:0001530 lipopolysaccharide binding and GO:0019956 chemokine binding. These binding activities collectively position the protein as a soluble pattern-recognition and inflammatory-modulatory factor.\n\nFrom these molecular activities, the biological processes follow. The ability to bind lipopolysaccharide and chemokines, coupled with extracellular signaling and integrin engagement, drives host defense pathways formalized as GO:0050829 defense response to Gram-negative bacterium and GO:0050830 defense response to Gram-positive bacterium. Inside the cell, damaged DNA binding and transcriptional modulation further reinforce stress-responsive immunity and repair.\n\nCellular localization is bifurcated by function. The chromatin-centric HMG-box core situates the protein in the GO:0005654 nucleoplasm and within GO:0017053 transcription repressor complex when it enforces repression. Its architectural role on mitotic chromatin supports presence at GO:0000793 condensed chromosome. Secretory and extracellular roles arise through unconventional trafficking: transient residence in GO:0005783 endoplasmic reticulum precedes secretion to the GO:0005615 extracellular space and deposition into GO:0034774 secretory granule lumen and GO:1904813 ficolin-1-rich granule lumen. At the plasma membrane, integrin binding places it at the GO:0009986 cell surface and within GO:0098797 plasma membrane protein complex.\n\nMechanistically, the tandem HMG boxes bend DNA and RNA to nucleate higher-order assemblies that switch between nuclear chromatin remodeling and extracellular signaling. In the nucleus, this architecture recruits transcriptional coactivators or corepressors and interfaces with polymerase II and DNA polymerases to tune gene expression and repair. Outside the cell, the same modular binding surfaces capture integrins and anionic lipids, and sequester inflammatory ligands such as chemokines and lipopolysaccharide, thereby modulating adhesion and innate immune pathways.\n\nThese deductions suggest likely interaction partners. In the nucleus, integrin-binding and defense-related binding predict associations with integrin heterodimers and membrane-associated complexes; transcriptional modulation predicts contacts with RNA polymerase II and DNA-binding transcription factors; and polymerase engagement predicts interactions with DNA polymerase assemblies. In the secretory/extracellular axis, associations with ficolin-1-rich granule machinery and integrin-containing membrane protein complexes are expected. Together, these partnerships unify chromatin architecture with immune and adhesion signaling.","category":"dark","control_evaluation":null,"validation_plan":null,"structure":{"source":"AlphaFold DB","pdb":"/structures/AF-B2RPK0.pdb","alphafold":"https://alphafold.ebi.ac.uk/entry/B2RPK0"},"links":{"uniprot":"https://www.uniprot.org/uniprotkb/B2RPK0/entry","atlas":"/p/B2RPK0"},"provenance":{"model":"BioReason-Pro (ESM3 esm3-sm-open-v1)","source_list":"Pharos Tdark","note":"AI prediction, not experimentally verified"}}