{"gene":"TXNL4B","run_date":"2026-06-10T10:51:56","timeline":{"discoveries":[{"year":2004,"finding":"DLP/TXNL4B (Dim1-like protein) localizes to the cell nucleus and interacts with the U5-102-kDa protein subunit of the spliceosome; knockdown of DLP activity leads to insufficient pre-mRNA splicing, and DLP is required for S/G2 cell cycle transition.","method":"Molecular cloning, subcellular localization experiments, protein-protein interaction assays, functional knockdown with pre-mRNA splicing readout and cell cycle analysis","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — single lab, multiple orthogonal methods (localization, interaction, splicing assay, cell cycle analysis) but no structural or reconstitution data","pmids":["15161931"],"is_preprint":false},{"year":2005,"finding":"The crystal structure of human TXNL4B (hDim2) at 2.5 Å resolution reveals a classical thioredoxin-fold with an extra α-helix (α3) and β-strand (β5) that stabilize the protein and may mediate interactions with hDim2-specific partners. Unlike hDim1, hDim2 forms stable homodimers stabilized by electrostatic interactions involving tyrosine residues in the α3 helix. hDim2 lacks structural motifs required for hDim1 biological activity, suggesting the two proteins participate in different multisubunit complexes.","method":"X-ray crystallography (2.5 Å), circular dichroism, fluorescence spectroscopy, size-exclusion chromatography, chemical cross-linking","journal":"Biochemistry","confidence":"High","confidence_rationale":"Tier 1 / Moderate — crystal structure solved with multiple orthogonal biophysical validations (CD, fluorescence, chromatography, cross-linking) in a single rigorous study","pmids":["16142897"],"is_preprint":false},{"year":2005,"finding":"TXNL4B was overexpressed, purified, and crystallized; crystals diffract to at least 1.50 Å, confirming the protein can be obtained in recombinant form suitable for structural analysis.","method":"Recombinant protein overexpression in E. coli, purification, vapor-diffusion crystallization, X-ray diffraction","journal":"Acta crystallographica. Section F, Structural biology and crystallization communications","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — structural crystallography established but this paper is primarily a methods/crystallization report without functional data","pmids":["16511018"],"is_preprint":false},{"year":2013,"finding":"High-resolution crystal structure of human TXNL4B (Dim2) determined at 1.33 Å reveals a thioredoxin-fold with one native dimer in the asymmetric unit. Structural analysis indicates that residues 1–33 (previously reported as the Prp6-interaction region) extend into the β-sheet core of the thioredoxin fold, casting doubt on the straightforward interpretation of prior GST pull-down data for this interaction region.","method":"X-ray crystallography (1.33 Å resolution)","journal":"Acta crystallographica. Section F, Structural biology and crystallization communications","confidence":"High","confidence_rationale":"Tier 1 / Moderate — high-resolution crystal structure (1.33 Å) of the human protein with structural interpretation of the Prp6-binding interface; single lab but rigorous structural method","pmids":["23519793"],"is_preprint":false},{"year":2023,"finding":"TXNL4B interacts with RNA processing factor 3 (PRP3) and the two proteins co-localize in the nucleus following ionizing radiation (IR). Nuclear PRP3 promotes alternative splicing of FANCI pre-mRNA to produce variants FANCI-12 and FANCI-13. TXNL4B knockdown increases cellular radiosensitivity, causes G2/M arrest, and delays DNA damage repair. Mechanistically, PRP3 promotes interaction of core spliceosome components PRP31 and PRP8; inhibition of PRP3 disrupts this interaction, suppresses FANCI-12 production, and impairs DNA damage repair.","method":"Co-immunoprecipitation, co-localization (nuclear), siRNA knockdown, alternative splicing analysis of FANCI variants, cell cycle analysis (G2/M arrest), clonogenic survival assay after IR","journal":"MedComm","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — single lab with multiple orthogonal methods (Co-IP, co-localization, knockdown with splicing readout, cell cycle and DNA repair phenotypes), but no in vitro reconstitution or structural validation","pmids":["37168687"],"is_preprint":false}],"current_model":"TXNL4B (DLP/hDim2) is a nuclear thioredoxin-fold protein that forms stable homodimers and functions as a spliceosomal component: it interacts with the U5-102-kDa spliceosomal subunit and with PRP3, participates in pre-mRNA splicing (including IR-induced alternative splicing of FANCI), and is required for S/G2 cell cycle progression, with its loss sensitizing cells to ionizing radiation by impairing DNA damage repair."},"narrative":{"mechanistic_narrative":"TXNL4B (DLP/hDim2) is a nuclear thioredoxin-fold protein that functions as a spliceosome-associated factor governing pre-mRNA splicing and cell cycle progression [PMID:15161931]. It adopts a classical thioredoxin fold elaborated by an extra α3 helix and β5 strand and, unlike its paralog hDim1, assembles into stable homodimers stabilized by electrostatic interactions involving tyrosine residues in the α3 helix; it lacks the structural motifs required for hDim1 activity, indicating that the two proteins act in distinct multisubunit complexes [PMID:16142897]. TXNL4B engages the spliceosome through interaction with the U5-102-kDa subunit, and its loss results in insufficient pre-mRNA splicing and failure of the S/G2 cell cycle transition [PMID:15161931]. Following ionizing radiation, TXNL4B interacts and co-localizes in the nucleus with the splicing factor PRP3, which drives alternative splicing of FANCI pre-mRNA; depletion of TXNL4B increases radiosensitivity, causes G2/M arrest, and delays DNA damage repair [PMID:37168687].","teleology":[{"year":2004,"claim":"Established TXNL4B as a nuclear spliceosome-associated protein by linking it physically to the splicing machinery and functionally to RNA processing and cell division.","evidence":"Molecular cloning with subcellular localization, interaction assays against the U5-102-kDa subunit, and knockdown with splicing and cell cycle readouts","pmids":["15161931"],"confidence":"Medium","gaps":["No structural basis for the U5-102-kDa interaction","Direct splicing substrates not identified","Mechanism linking splicing role to S/G2 transition unresolved"]},{"year":2005,"claim":"Defined the molecular architecture that distinguishes TXNL4B from its paralog, showing it is a homodimeric thioredoxin-fold protein lacking hDim1 activity motifs and thus likely acting in a different complex.","evidence":"X-ray crystallography at 2.5 Å with CD, fluorescence, size-exclusion chromatography and cross-linking; complemented by a high-quality recombinant crystallization report","pmids":["16142897","16511018"],"confidence":"High","gaps":["Functional consequence of homodimerization in splicing not tested","hDim2-specific partner predicted from α3/β5 elements not identified"]},{"year":2013,"claim":"Refined the structure to near-atomic resolution and reinterpreted the proposed Prp6-binding region, showing residues 1–33 are buried in the fold core rather than freely available for interaction.","evidence":"X-ray crystallography at 1.33 Å resolution with structural mapping of the previously assigned interaction region","pmids":["23519793"],"confidence":"High","gaps":["Does not define the true Prp6 interaction surface","No co-complex structure with any spliceosomal partner"]},{"year":2023,"claim":"Connected TXNL4B to the DNA damage response by tying its splicing function, via PRP3, to alternative splicing of FANCI and to radiation sensitivity.","evidence":"Co-IP, nuclear co-localization, siRNA knockdown with FANCI splice-variant analysis, cell cycle profiling, and clonogenic survival after ionizing radiation","pmids":["37168687"],"confidence":"Medium","gaps":["No in vitro reconstitution of TXNL4B/PRP3 action on FANCI splicing","Direct catalytic or scaffolding role of TXNL4B not separated from PRP3 activity","Structural basis of TXNL4B–PRP3 interaction unknown"]},{"year":null,"claim":"How the homodimeric thioredoxin fold of TXNL4B is mechanistically deployed within the spliceosome, and whether it acts catalytically or as a scaffold, remains undefined.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No co-complex structure with U5-102-kDa, PRP3, or other spliceosomal subunits","No defined enzymatic activity for the thioredoxin fold","Direct vs indirect contribution to DNA repair not resolved"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140098","term_label":"catalytic activity, acting on RNA","supporting_discovery_ids":[0,4]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[0,4]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[0,4]}],"complexes":["spliceosome"],"partners":["PRP3","PRPF6"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9NX01","full_name":"Thioredoxin-like protein 4B","aliases":["Dim1-like protein"],"length_aa":149,"mass_kda":17.0,"function":"Essential role in pre-mRNA splicing. Required in cell cycle progression for S/G(2) transition","subcellular_location":"Nucleus","url":"https://www.uniprot.org/uniprotkb/Q9NX01/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/TXNL4B","classification":"Common Essential","n_dependent_lines":1036,"n_total_lines":1208,"dependency_fraction":0.8576158940397351},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/TXNL4B","total_profiled":1310},"omim":[{"mim_id":"617754","title":"RIO KINASE 2; RIOK2","url":"https://www.omim.org/entry/617754"},{"mim_id":"617722","title":"THIOREDOXIN-LIKE 4B; TXNL4B","url":"https://www.omim.org/entry/617722"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoplasm","reliability":"Supported"},{"location":"Cytosol","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/TXNL4B"},"hgnc":{"alias_symbol":["FLJ20511","DLP","Dim2"],"prev_symbol":[]},"alphafold":{"accession":"Q9NX01","domains":[{"cath_id":"3.40.30.10","chopping":"6-136","consensus_level":"high","plddt":96.3142,"start":6,"end":136}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9NX01","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9NX01-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9NX01-F1-predicted_aligned_error_v6.png","plddt_mean":92.56},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=TXNL4B","jax_strain_url":"https://www.jax.org/strain/search?query=TXNL4B"},"sequence":{"accession":"Q9NX01","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9NX01.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9NX01/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9NX01"}},"corpus_meta":[{"pmid":"11483533","id":"PMC_11483533","title":"dim-2 encodes a DNA methyltransferase responsible for all known cytosine methylation in Neurospora.","date":"2001","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/11483533","citation_count":162,"is_preprint":false},{"pmid":"32228893","id":"PMC_32228893","title":"Fabrication of liver microtissue with liver decellularized extracellular matrix (dECM) bioink by digital light processing (DLP) bioprinting.","date":"2020","source":"Materials science & engineering. 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   \"year\": 2004,\n      \"finding\": \"DLP/TXNL4B (Dim1-like protein) localizes to the cell nucleus and interacts with the U5-102-kDa protein subunit of the spliceosome; knockdown of DLP activity leads to insufficient pre-mRNA splicing, and DLP is required for S/G2 cell cycle transition.\",\n      \"method\": \"Molecular cloning, subcellular localization experiments, protein-protein interaction assays, functional knockdown with pre-mRNA splicing readout and cell cycle analysis\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — single lab, multiple orthogonal methods (localization, interaction, splicing assay, cell cycle analysis) but no structural or reconstitution data\",\n      \"pmids\": [\"15161931\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"The crystal structure of human TXNL4B (hDim2) at 2.5 Å resolution reveals a classical thioredoxin-fold with an extra α-helix (α3) and β-strand (β5) that stabilize the protein and may mediate interactions with hDim2-specific partners. Unlike hDim1, hDim2 forms stable homodimers stabilized by electrostatic interactions involving tyrosine residues in the α3 helix. hDim2 lacks structural motifs required for hDim1 biological activity, suggesting the two proteins participate in different multisubunit complexes.\",\n      \"method\": \"X-ray crystallography (2.5 Å), circular dichroism, fluorescence spectroscopy, size-exclusion chromatography, chemical cross-linking\",\n      \"journal\": \"Biochemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — crystal structure solved with multiple orthogonal biophysical validations (CD, fluorescence, chromatography, cross-linking) in a single rigorous study\",\n      \"pmids\": [\"16142897\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"TXNL4B was overexpressed, purified, and crystallized; crystals diffract to at least 1.50 Å, confirming the protein can be obtained in recombinant form suitable for structural analysis.\",\n      \"method\": \"Recombinant protein overexpression in E. coli, purification, vapor-diffusion crystallization, X-ray diffraction\",\n      \"journal\": \"Acta crystallographica. Section F, Structural biology and crystallization communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — structural crystallography established but this paper is primarily a methods/crystallization report without functional data\",\n      \"pmids\": [\"16511018\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"High-resolution crystal structure of human TXNL4B (Dim2) determined at 1.33 Å reveals a thioredoxin-fold with one native dimer in the asymmetric unit. Structural analysis indicates that residues 1–33 (previously reported as the Prp6-interaction region) extend into the β-sheet core of the thioredoxin fold, casting doubt on the straightforward interpretation of prior GST pull-down data for this interaction region.\",\n      \"method\": \"X-ray crystallography (1.33 Å resolution)\",\n      \"journal\": \"Acta crystallographica. Section F, Structural biology and crystallization communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — high-resolution crystal structure (1.33 Å) of the human protein with structural interpretation of the Prp6-binding interface; single lab but rigorous structural method\",\n      \"pmids\": [\"23519793\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"TXNL4B interacts with RNA processing factor 3 (PRP3) and the two proteins co-localize in the nucleus following ionizing radiation (IR). Nuclear PRP3 promotes alternative splicing of FANCI pre-mRNA to produce variants FANCI-12 and FANCI-13. TXNL4B knockdown increases cellular radiosensitivity, causes G2/M arrest, and delays DNA damage repair. Mechanistically, PRP3 promotes interaction of core spliceosome components PRP31 and PRP8; inhibition of PRP3 disrupts this interaction, suppresses FANCI-12 production, and impairs DNA damage repair.\",\n      \"method\": \"Co-immunoprecipitation, co-localization (nuclear), siRNA knockdown, alternative splicing analysis of FANCI variants, cell cycle analysis (G2/M arrest), clonogenic survival assay after IR\",\n      \"journal\": \"MedComm\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — single lab with multiple orthogonal methods (Co-IP, co-localization, knockdown with splicing readout, cell cycle and DNA repair phenotypes), but no in vitro reconstitution or structural validation\",\n      \"pmids\": [\"37168687\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"TXNL4B (DLP/hDim2) is a nuclear thioredoxin-fold protein that forms stable homodimers and functions as a spliceosomal component: it interacts with the U5-102-kDa spliceosomal subunit and with PRP3, participates in pre-mRNA splicing (including IR-induced alternative splicing of FANCI), and is required for S/G2 cell cycle progression, with its loss sensitizing cells to ionizing radiation by impairing DNA damage repair.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"TXNL4B (DLP/hDim2) is a nuclear thioredoxin-fold protein that functions as a spliceosome-associated factor governing pre-mRNA splicing and cell cycle progression [#0]. It adopts a classical thioredoxin fold elaborated by an extra \\u03b13 helix and \\u03b25 strand and, unlike its paralog hDim1, assembles into stable homodimers stabilized by electrostatic interactions involving tyrosine residues in the \\u03b13 helix; it lacks the structural motifs required for hDim1 activity, indicating that the two proteins act in distinct multisubunit complexes [#1]. TXNL4B engages the spliceosome through interaction with the U5-102-kDa subunit, and its loss results in insufficient pre-mRNA splicing and failure of the S/G2 cell cycle transition [#0]. Following ionizing radiation, TXNL4B interacts and co-localizes in the nucleus with the splicing factor PRP3, which drives alternative splicing of FANCI pre-mRNA; depletion of TXNL4B increases radiosensitivity, causes G2/M arrest, and delays DNA damage repair [#4].\",\n  \"teleology\": [\n    {\n      \"year\": 2004,\n      \"claim\": \"Established TXNL4B as a nuclear spliceosome-associated protein by linking it physically to the splicing machinery and functionally to RNA processing and cell division.\",\n      \"evidence\": \"Molecular cloning with subcellular localization, interaction assays against the U5-102-kDa subunit, and knockdown with splicing and cell cycle readouts\",\n      \"pmids\": [\"15161931\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structural basis for the U5-102-kDa interaction\", \"Direct splicing substrates not identified\", \"Mechanism linking splicing role to S/G2 transition unresolved\"]\n    },\n    {\n      \"year\": 2005,\n      \"claim\": \"Defined the molecular architecture that distinguishes TXNL4B from its paralog, showing it is a homodimeric thioredoxin-fold protein lacking hDim1 activity motifs and thus likely acting in a different complex.\",\n      \"evidence\": \"X-ray crystallography at 2.5 \\u00c5 with CD, fluorescence, size-exclusion chromatography and cross-linking; complemented by a high-quality recombinant crystallization report\",\n      \"pmids\": [\"16142897\", \"16511018\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Functional consequence of homodimerization in splicing not tested\", \"hDim2-specific partner predicted from \\u03b13/\\u03b25 elements not identified\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Refined the structure to near-atomic resolution and reinterpreted the proposed Prp6-binding region, showing residues 1\\u201333 are buried in the fold core rather than freely available for interaction.\",\n      \"evidence\": \"X-ray crystallography at 1.33 \\u00c5 resolution with structural mapping of the previously assigned interaction region\",\n      \"pmids\": [\"23519793\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Does not define the true Prp6 interaction surface\", \"No co-complex structure with any spliceosomal partner\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Connected TXNL4B to the DNA damage response by tying its splicing function, via PRP3, to alternative splicing of FANCI and to radiation sensitivity.\",\n      \"evidence\": \"Co-IP, nuclear co-localization, siRNA knockdown with FANCI splice-variant analysis, cell cycle profiling, and clonogenic survival after ionizing radiation\",\n      \"pmids\": [\"37168687\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No in vitro reconstitution of TXNL4B/PRP3 action on FANCI splicing\", \"Direct catalytic or scaffolding role of TXNL4B not separated from PRP3 activity\", \"Structural basis of TXNL4B\\u2013PRP3 interaction unknown\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How the homodimeric thioredoxin fold of TXNL4B is mechanistically deployed within the spliceosome, and whether it acts catalytically or as a scaffold, remains undefined.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No co-complex structure with U5-102-kDa, PRP3, or other spliceosomal subunits\", \"No defined enzymatic activity for the thioredoxin fold\", \"Direct vs indirect contribution to DNA repair not resolved\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140098\", \"supporting_discovery_ids\": [0, 4]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [0, 4]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [0, 4]}\n    ],\n    \"complexes\": [\"spliceosome\"],\n    \"partners\": [\"PRP3\", \"PRPF6\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":4,"faith_total":4,"faith_pct":100.0}}