{"database":"JPOST Repository","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Xlsx":["https://storage.jpostdb.org/JPST001057/files/Xkr4_SPOTtrap_LFQ.xlsx"],"Raw":["https://storage.jpostdb.org/JPST001057/files/4_XRCC4_R270A_STS.raw","https://storage.jpostdb.org/JPST001057/files/3_XRCC4_R270A_minus.raw","https://storage.jpostdb.org/JPST001057/files/1_XRCC4_WT_minus.raw","https://storage.jpostdb.org/JPST001057/files/2_XRCC4_WT_STS.raw"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"omics_type":["Proteomics"],"submitter":["Hidetaka Kosako"],"species":["Homo Sapiens (human)"],"full_dataset_link":["https://repository.jpostdb.org/entry/JPST001057"],"submitter_affiliation":["Tokushima University"],"sample_protocol":[""],"repository":["jPOST"],"data_protocol":[""],"pubmed_abstract":["Phospholipid scrambling in dying cells promotes phosphatidylserine exposure, a critical process for efferocytosis. We previously identified the Xkr family protein Xkr4 as a phospholipid-scrambling protein, but its activation mechanisms remain unknown. Here we show that Xkr4 is activated in two steps: dimer formation by caspase-mediated cleavage and structural change caused by activating factors. To identify the factors, we developed a new screening system, \"revival screening,\" using a CRISPR sgRNA library. Applying this system, we identified the nuclear protein XRCC4 as the single candidate for the Xkr4 activator. Upon apoptotic stimuli, XRCC4, contained in the DNA repair complex, is cleaved by caspases, and its C-terminal fragment with an intrinsically disordered region is released into the cytoplasm. Protein interaction screening showed that the fragment interacts directly with the Xkr4 dimer to activate it. This study demonstrates that caspase-mediated cleavage releases a nuclear protein fragment for direct regulation of lipid dynamics on the plasma membrane."],"pubmed_title":["Caspase cleavage releases a nuclear protein fragment that stimulates phospholipid scrambling at the plasma membrane."],"pubmed_authors":["Maruoka Masahiro M, Zhang Panpan P, Mori Hiromi H, Imanishi Eiichi E, Packwood Daniel M DM, Harada Hiroshi H, Kosako Hidetaka H, Suzuki Jun J"],"name_synonyms":["Gm210, AY534250, LFQ, XRG4., mKIAA1889"],"pubmed_abstract_synonyms":["Networks, Regulations, lipids, apoptotic cell removal, Plasma Membranes, efferocytosis, Family Member, Kinship, phospholipids, 2310057B22Rik, Cytoplasmic Membrane, Gm210, cleavage, Gene, Network, protein, protein-containing complex, Social Controls, Protoplasm, protrusion, Gene Products, Phosphatidyl, Life Cycle, protein aggregate, Apoptotic Cell Clearance, WHY1 complex, Formal Social Controls, Family Life Cycle, multicellular organismal biosynthetic process, study, single-organism biosynthetic process, anatomical systems, Kinship Network, Phospholipid, Apoptotic Cell, Clearance, Research, Social, Cytoplasmic, plasma membrane lipid bilayer, Caspase, Cytoplasmic Membranes, plasmalemma, XRG4, Plasma Membrane, site, Kinship Networks, Family Life Cycles, Family, integral to plasma membrane, inner endospore membrane., anatomical protrusion, Family Research, DNA damage repair complex, mKIAA1889, Formal Social Control, protein complex, phospholipid scrambling, Cytoplasms, integral component of plasma membrane, Proteins, flippase, Phosphoglycerides, Phosphatides, Apoptotic Cell Clearances, Cell, Family Members, AW545101, cellular membrane, Serines, native protein, Social Control, Cell Clearances, Apoptotic, Protein, Lipid, sequence, Serine Phosphoglycerides, bacterial inner membrane, Filiation, Cell Membranes, Library, activation, region, Plasma, a phospholipid derivative, Membranes, Serine, cell membrane, programmed cell clearance, Clearances, AW413319, Cell Clearance, Control, Phosphatidyl Serines, Controls, Membrane, Phosphatidylserine, primary structure of sequence macromolecule, Protein Gene Products, AY534250, Life Cycles, Gene Proteins, spine, Families, Protoplasms, regulation, cytoplasmic membrane, Relatives, Regulation, Phosphatidyl Serine"],"pubmed_title_synonyms":["Plasma, Membranes, Plasma Membranes, inner endospore membrane., cell membrane, protein complex, phospholipid scrambling, integral component of plasma membrane, Proteins, Cytoplasmic Membrane, cleavage, Gene, flippase, protein, Membrane, protein-containing complex, Cell, Protein Gene Products, Cytoplasmic, Gene Proteins, plasma membrane lipid bilayer, cellular membrane, Caspase, native protein, Cytoplasmic Membranes, plasmalemma, Protein, Gene Products, Plasma Membrane, bacterial inner membrane, cytoplasmic membrane, protein aggregate, Cell Membranes, integral to plasma membrane"],"description_synonyms":["Membrane Tissue, membrane, Detergent Pod, C6orf190, mKIAA1889, Laundry Detergent Pods, 2310057B22Rik, CMD1P, Laundry Pods, Synthetic Detergents, CMH18, Gm210, integral to membrane, Syndet, GASP, Spectrum Analyses, Spectrum Analysis, Cell, Agent, Spectroscopy, AW545101, Membrane Tissues, Detergent, SPOT, Pod, Synthetic Detergent, MS, integral component of membrane, Detergents, whole membrane, Mass, bA325O24.4, Laundry Detergent Pod, Cleansing Agents, Analysis, spot, Detergent Pods, Mass Spectrum Analyses, Mass Spectroscopy, Cleansing, Mass Spectrum Analysis, Synthetic, Mass Spectrum, transmembrane, PLB, Pods, Analyses, AW413319, Tissues, bA325O24.3, membrane region, Tissue, TSEPA, Spectrometry, C6orf207, Membrane, Laundry Detergent, AY534250, Agents, Cleansing Agent, precipited material, XRG4, region of membrane, Mass., Laundry Pod, Laundry"],"additional_accession":[]},"is_claimable":false,"name":"Label-free quantification of Xkr4 interactors","description":"Membrane fractions of XRCC4 KO PLB cells expressing SPOT-Xkr4-FLAG and XRCC4 (WT or R270A) were solubilized by detergent and immunoprecipitated with anti-SPOT nanobody-conjugated beads to precipitate Xkr4 interactors, followed by mass spectrometry.","dates":{"publication":"Tue Jan 12 00:00:00 GMT 2021"},"accession":"PXD023536","cross_references":{"TAXONOMY":["9606"],"pubmed":["33725486"]}}