{"gene":"PF3D7_0323500","run_date":"2026-09-08T16:26:55","timeline":{"discoveries":[{"year":2013,"finding":"PF3D7_0323500 (PfSMN, survival of motor neuron-like protein) physically interacts with PfSmD1 (a spliceosome core Sm protein) in P. falciparum, and this interaction is methylation-dependent, as demonstrated by yeast two-hybrid analysis and in vitro pull-down assays.","method":"Yeast two-hybrid analysis and in vitro pull-down assays","journal":"Malaria journal","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal yeast two-hybrid and pull-down, single lab, two orthogonal methods but no mutagenesis or structural validation","pmids":["24047207"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2007,"finding":"PF3D7_0323500 (SMN-like protein) was identified as a Tudor domain-containing protein in P. falciparum; its existence in Plasmodium and other protozoan parasites was established by sequence and domain analysis, though functional characterization of the SMN protein itself was not performed in this study.","method":"Bioinformatic sequence analysis and domain identification","journal":"International journal for parasitology","confidence":"Low","confidence_rationale":"Tier 4 / Weak — computational/sequence identification only, no functional experiment performed on the SMN protein itself","pmids":["18035357"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"current_model":"In P. falciparum, PF3D7_0323500 (SMN) is a Tudor domain-containing protein that participates in spliceosome assembly by physically interacting with the core Sm protein PfSmD1 in a methylation-dependent manner, placing it functionally within the cytoplasmic snRNP biogenesis pathway."},"narrative":{"mechanistic_narrative":"In P. falciparum, PF3D7_0323500 (SMN) is a Tudor domain-containing protein that functions in the assembly of spliceosomal small nuclear ribonucleoproteins by engaging the core Sm protein machinery [PMID:24047207, PMID:18035357]. It physically interacts with PfSmD1, a spliceosome core Sm protein, and this interaction is methylation-dependent, placing PF3D7_0323500 at the interface of snRNP biogenesis where methylated Sm proteins are recognized and assembled [PMID:24047207]. Beyond this methylation-dependent association with PfSmD1, no further mechanistic detail — including in vivo function, structural basis of recognition, or the full complement of interacting partners — has been characterized for PF3D7_0323500 in the available corpus.","teleology":[{"year":2007,"claim":"Before any functional work, it was unknown whether Plasmodium encodes an SMN-type protein at all; domain analysis established the existence of a Tudor domain-containing SMN-like protein in the parasite, providing the molecular entity later work would characterize.","evidence":"Bioinformatic sequence analysis and domain identification in P. falciparum","pmids":["18035357"],"confidence":"Low","gaps":["Computational identification only; no functional experiment was performed on the SMN protein itself","Domain presence does not establish that the protein participates in snRNP assembly","No expression, localization, or interaction data"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2013,"claim":"Having a candidate SMN protein, it was unknown whether it engages the spliceosomal Sm core; reciprocal binding assays showed a methylation-dependent interaction with PfSmD1, establishing PF3D7_0323500 as a functional participant in snRNP biogenesis rather than a mere sequence homolog.","evidence":"Yeast two-hybrid analysis and in vitro pull-down assays in P. falciparum","pmids":["24047207"],"confidence":"Medium","gaps":["Interaction shown by two orthogonal in vitro methods from a single lab; no mutagenesis mapping the binding interface or structural validation","In vivo relevance of the interaction during the parasite life cycle not tested","Which methyltransferase generates the methylation mark, and whether other Sm proteins are recognized, is not addressed"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":null,"claim":"The in vivo role of PF3D7_0323500 in P. falciparum splicing and parasite viability, its full interactome, and the structural basis of its methylation-dependent Sm recognition remain uncharacterized.","evidence":"","pmids":[],"confidence":"Low","gaps":["No knockout, knockdown, or conditional-depletion phenotype reported","No structural model of the Tudor domain bound to methylated PfSmD1","No evidence linking PF3D7_0323500 to specific splicing events or parasite developmental stages"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":[],"partners":["PFSMD1 (SPLICEOSOME CORE SM PROTEIN; METHYLATION-DEPENDENT INTERACTION) [#0]"],"other_free_text":["PF3D7_0323500 is a Tudor domain-containing protein identified in P. falciparum by sequence and domain analysis [#1].","The interaction with PfSmD1 is methylation-dependent, consistent with Tudor-domain recognition of methylated Sm proteins [#0]."]}},"prefetch_data":{},"corpus_meta":[{"pmid":"18035357","id":"PMC_18035357","title":"Tudor domain proteins in protozoan parasites and characterization of Plasmodium falciparum tudor staphylococcal nuclease.","date":"2007","source":"International journal for parasitology","url":"https://pubmed.ncbi.nlm.nih.gov/18035357","citation_count":27,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["SMN"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"24047207","id":"","title":"Organization of Plasmodium falciparum spliceosomal core complex and role of arginine methylation in its assembly.","date":"2013","source":"Malaria journal","url":"https://pubmed.ncbi.nlm.nih.gov/24047207","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["SMN"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"34855919","id":"","title":"\"Reading\" a new chapter in protozoan parasite transcriptional regulation.","date":"2021","source":"PLoS pathogens","url":"https://pubmed.ncbi.nlm.nih.gov/34855919","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["SMN"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"29364142","id":"","title":"Current Perspectives of Telomerase Structure and Function in Eukaryotes with Emerging Views on Telomerase in Human Parasites.","date":"2018","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/29364142","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["SMN"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"19282982","id":"","title":"Sm/Lsm genes provide a glimpse into the early evolution of the spliceosome.","date":"2009","source":"PLoS computational biology","url":"https://pubmed.ncbi.nlm.nih.gov/19282982","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["SMN"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"22573172","id":"","title":"Structural bioinformatics of the human spliceosomal proteome.","date":"2012","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/22573172","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["SMN"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":8584,"output_tokens":571,"usd":0.017159,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5136,"output_tokens":1539,"usd":0.032078,"stage2_stop_reason":"end_turn"},"total_usd":0.049237,"stage1_batch_id":"msgbatch_01NE1MTa8x1hW7Lo4tAaNzY1","stage2_batch_id":"msgbatch_0141vaQdeFvbo2q39AinvXM9","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2013,\n      \"finding\": \"PF3D7_0323500 (PfSMN, survival of motor neuron-like protein) physically interacts with PfSmD1 (a spliceosome core Sm protein) in P. falciparum, and this interaction is methylation-dependent, as demonstrated by yeast two-hybrid analysis and in vitro pull-down assays.\",\n      \"method\": \"Yeast two-hybrid analysis and in vitro pull-down assays\",\n      \"journal\": \"Malaria journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal yeast two-hybrid and pull-down, single lab, two orthogonal methods but no mutagenesis or structural validation\",\n      \"pmids\": [\"24047207\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"PF3D7_0323500 (SMN-like protein) was identified as a Tudor domain-containing protein in P. falciparum; its existence in Plasmodium and other protozoan parasites was established by sequence and domain analysis, though functional characterization of the SMN protein itself was not performed in this study.\",\n      \"method\": \"Bioinformatic sequence analysis and domain identification\",\n      \"journal\": \"International journal for parasitology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 4 / Weak — computational/sequence identification only, no functional experiment performed on the SMN protein itself\",\n      \"pmids\": [\"18035357\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"current_model\": \"In P. falciparum, PF3D7_0323500 (SMN) is a Tudor domain-containing protein that participates in spliceosome assembly by physically interacting with the core Sm protein PfSmD1 in a methylation-dependent manner, placing it functionally within the cytoplasmic snRNP biogenesis pathway.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"In P. falciparum, PF3D7_0323500 (SMN) is a Tudor domain-containing protein that functions in the assembly of spliceosomal small nuclear ribonucleoproteins by engaging the core Sm protein machinery [#0, #1]. It physically interacts with PfSmD1, a spliceosome core Sm protein, and this interaction is methylation-dependent, placing PF3D7_0323500 at the interface of snRNP biogenesis where methylated Sm proteins are recognized and assembled [#0]. Beyond this methylation-dependent association with PfSmD1, no further mechanistic detail — including in vivo function, structural basis of recognition, or the full complement of interacting partners — has been characterized for PF3D7_0323500 in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2007,\n      \"claim\": \"Before any functional work, it was unknown whether Plasmodium encodes an SMN-type protein at all; domain analysis established the existence of a Tudor domain-containing SMN-like protein in the parasite, providing the molecular entity later work would characterize.\",\n      \"evidence\": \"Bioinformatic sequence analysis and domain identification in P. falciparum\",\n      \"pmids\": [\n        \"18035357\"\n      ],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"Computational identification only; no functional experiment was performed on the SMN protein itself\",\n        \"Domain presence does not establish that the protein participates in snRNP assembly\",\n        \"No expression, localization, or interaction data\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Plasmodium falciparum\",\n          \"strain\": \"\"\n        }\n      ]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Having a candidate SMN protein, it was unknown whether it engages the spliceosomal Sm core; reciprocal binding assays showed a methylation-dependent interaction with PfSmD1, establishing PF3D7_0323500 as a functional participant in snRNP biogenesis rather than a mere sequence homolog.\",\n      \"evidence\": \"Yeast two-hybrid analysis and in vitro pull-down assays in P. falciparum\",\n      \"pmids\": [\n        \"24047207\"\n      ],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Interaction shown by two orthogonal in vitro methods from a single lab; no mutagenesis mapping the binding interface or structural validation\",\n        \"In vivo relevance of the interaction during the parasite life cycle not tested\",\n        \"Which methyltransferase generates the methylation mark, and whether other Sm proteins are recognized, is not addressed\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Plasmodium falciparum\",\n          \"strain\": \"\"\n        }\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The in vivo role of PF3D7_0323500 in P. falciparum splicing and parasite viability, its full interactome, and the structural basis of its methylation-dependent Sm recognition remain uncharacterized.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No knockout, knockdown, or conditional-depletion phenotype reported\",\n        \"No structural model of the Tudor domain bound to methylated PfSmD1\",\n        \"No evidence linking PF3D7_0323500 to specific splicing events or parasite developmental stages\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Plasmodium falciparum\",\n          \"strain\": \"\"\n        }\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\n        \"term_id\": \"GO:0030674\",\n        \"supporting_discovery_ids\": [\n          0\n        ]\n      }\n    ],\n    \"localization\": [],\n    \"pathway\": [\n      {\n        \"term_id\": \"GO:0000387\",\n        \"supporting_discovery_ids\": [\n          0\n        ]\n      }\n    ],\n    \"complexes\": [],\n    \"partners\": [\n      \"PfSmD1 (spliceosome core Sm protein; methylation-dependent interaction) [#0]\"\n    ],\n    \"other_free_text\": [\n      \"PF3D7_0323500 is a Tudor domain-containing protein identified in P. falciparum by sequence and domain analysis [#1].\",\n      \"The interaction with PfSmD1 is methylation-dependent, consistent with Tudor-domain recognition of methylated Sm proteins [#0].\"\n    ]\n  }\n}","audit_flag":null,"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_0323500","name":null,"product":"survival motor neuron-like protein","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_1215000","name":null,"product":"survival motor neuron-like protein, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_0816900","name":null,"product":"survival motor neuron-like protein, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"SMN","evaluation":null}