{"gene":"PF3D7_1125500","run_date":"2026-09-08T19:44:17","timeline":{"discoveries":[{"year":2010,"finding":"PfSmD1 (SNRPD1/PF3D7_1125500) interacts with the Tudor domain of PfTudor-SN (PfTu-TSN) in a yeast two-hybrid screen, suggesting a role for SNRPD1 in spliceosome assembly in P. falciparum asexual blood stages.","method":"Yeast two-hybrid assay","journal":"Gene","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single yeast two-hybrid result, single lab, no orthogonal validation of the SNRPD1-specific interaction reported in abstract","pmids":["20713134"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2013,"finding":"SNRPD1 (PfSmD1) is expressed at asexual blood stages and shows nucleo-cytoplasmic localization. It participates in a heptameric Sm core complex typical of the spliceosome, with the arrangement of PfSm proteins slightly differing from the human complex.","method":"Immunofluorescence, western blotting, yeast two-hybrid, in vitro pull-down assays","journal":"Malaria journal","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — multiple orthogonal methods (IFA, western blot, yeast two-hybrid, pull-down) in a single lab confirming expression, localization, and complex membership","pmids":["24047207"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2013,"finding":"Interaction of SNRPD1 (PfSmD1) with PfSMN (survival of motor neuron, tudor domain-containing protein) is methylation-dependent, as shown by pull-down assays. PfPRMT5 (arginine methyltransferase) associates with SNRPD1 by co-immunoprecipitation, indicating arginine methylation of SNRPD1 (or its partners) is required for spliceosomal Sm core complex assembly in the cytoplasm.","method":"In vitro pull-down assays, co-immunoprecipitation, MALDI-TOF spectrometry","journal":"Malaria journal","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal pull-down and co-IP with mass spectrometry identification, single lab, two orthogonal methods","pmids":["24047207"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"current_model":"In P. falciparum, SNRPD1 (PfSmD1/PF3D7_1125500) is a nucleo-cytoplasmic Sm-like protein that forms part of a heptameric spliceosomal core complex; its interaction with the Tudor-domain protein PfSMN is methylation-dependent, and it associates with the arginine methyltransferase PfPRMT5, implicating arginine methylation in cytoplasmic assembly of the Sm core complex."},"narrative":{"mechanistic_narrative":"SNRPD1 (PfSmD1/PF3D7_1125500) is an Sm-class spliceosomal core protein of P. falciparum that assembles into a heptameric Sm core complex resembling, with a slightly altered subunit arrangement, the human spliceosomal Sm ring [PMID:24047207]. It is expressed in asexual blood stages and displays nucleo-cytoplasmic localization, consistent with cytoplasmic Sm-core assembly followed by nuclear function [PMID:24047207]. Its incorporation into this complex is governed by arginine methylation: SNRPD1 interacts with the Tudor-domain SMN protein PfSMN in a methylation-dependent manner and associates with the arginine methyltransferase PfPRMT5, implicating methylation-dependent recognition in cytoplasmic assembly of the Sm core [PMID:24047207]. Beyond its membership in the Sm core complex and these methylation-dependent partner interactions, no further mechanistic detail about SNRPD1 has been characterized in the available corpus.","teleology":[{"year":2010,"claim":"To place SNRPD1 within the parasite's RNA-processing machinery, an early interaction screen asked which proteins bind it, linking it to spliceosome assembly.","evidence":"Yeast two-hybrid screen identifying an interaction with the Tudor domain of PfTudor-SN in P. falciparum","pmids":["20713134"],"confidence":"Low","gaps":["Single yeast two-hybrid result with no orthogonal validation of the SNRPD1-specific interaction","Functional consequence of the PfTudor-SN interaction not tested","No demonstration that this interaction occurs in vivo in blood stages"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2013,"claim":"To establish whether SNRPD1 is a bona fide Sm-core subunit, its expression, localization, and complex membership were characterized, defining a parasite heptameric Sm core complex.","evidence":"Immunofluorescence, western blotting, yeast two-hybrid, and in vitro pull-down assays in P. falciparum asexual blood stages","pmids":["24047207"],"confidence":"Medium","gaps":["Stoichiometry and exact subunit arrangement of the parasite complex not resolved structurally","Direct role of SNRPD1 in snRNP assembly or pre-mRNA splicing not functionally tested","No genetic knockdown/knockout to assess essentiality"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2013,"claim":"To determine how Sm core assembly is regulated, the methylation dependence of SNRPD1's partner interactions was tested, implicating arginine methylation in cytoplasmic Sm-core assembly.","evidence":"In vitro pull-down, co-immunoprecipitation, and MALDI-TOF identification of methylation-dependent PfSMN binding and PfPRMT5 association in P. falciparum","pmids":["24047207"],"confidence":"Medium","gaps":["Direct arginine-methylated residues on SNRPD1 not mapped","Whether PfPRMT5 methylates SNRPD1 itself versus its partners not distinguished","In vivo requirement of methylation for splicing not established"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":null,"claim":"The functional role of SNRPD1 in pre-mRNA splicing and parasite viability, and the structural basis of the parasite Sm core, remain undefined.","evidence":"","pmids":[],"confidence":"Low","gaps":["No genetic loss-of-function data on SNRPD1 in any parasite stage","No structural model of the parasite Sm heptamer","No direct demonstration of SNRPD1 function in splicing"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["Heptameric spliceosomal Sm core complex"],"partners":["PFTUDOR-SN (PFTU-TSN)","PFSMN (SURVIVAL OF MOTOR NEURON, TUDOR-DOMAIN PROTEIN)","PFPRMT5 (ARGININE METHYLTRANSFERASE)"],"other_free_text":["Interaction with PfSMN is methylation-dependent, implicating arginine methylation in cytoplasmic Sm-core assembly [#2]","Parasite Sm core complex subunit arrangement differs slightly from the human complex [#1]"]}},"prefetch_data":{},"corpus_meta":[{"pmid":"20713134","id":"PMC_20713134","title":"Plasmodium falciparum Tudor Staphylococcal Nuclease interacting proteins suggest its role in nuclear as well as splicing processes.","date":"2010","source":"Gene","url":"https://pubmed.ncbi.nlm.nih.gov/20713134","citation_count":15,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["curated_ref"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"24047207","id":"PMC_24047207","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":12,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["curated_ref"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"36582189","id":"","title":"Combining IP3 affinity chromatography and bioinformatics reveals a novel protein-IP3 binding site on Plasmodium falciparum MDR1 transporter.","date":"2022","source":"Current research in microbial sciences","url":"https://pubmed.ncbi.nlm.nih.gov/36582189","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["SNRPD1"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":5293,"output_tokens":917,"usd":0.014817,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5615,"output_tokens":1896,"usd":0.037738,"stage2_stop_reason":"end_turn"},"total_usd":0.052555,"stage1_batch_id":"msgbatch_01SRp5hyRc82zNjddxyCCXGk","stage2_batch_id":"msgbatch_01K3BTmBazRo3pRrMvyaPMTY","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2010,\n      \"finding\": \"PfSmD1 (SNRPD1/PF3D7_1125500) interacts with the Tudor domain of PfTudor-SN (PfTu-TSN) in a yeast two-hybrid screen, suggesting a role for SNRPD1 in spliceosome assembly in P. falciparum asexual blood stages.\",\n      \"method\": \"Yeast two-hybrid assay\",\n      \"journal\": \"Gene\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single yeast two-hybrid result, single lab, no orthogonal validation of the SNRPD1-specific interaction reported in abstract\",\n      \"pmids\": [\"20713134\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"SNRPD1 (PfSmD1) is expressed at asexual blood stages and shows nucleo-cytoplasmic localization. It participates in a heptameric Sm core complex typical of the spliceosome, with the arrangement of PfSm proteins slightly differing from the human complex.\",\n      \"method\": \"Immunofluorescence, western blotting, yeast two-hybrid, in vitro pull-down assays\",\n      \"journal\": \"Malaria journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — multiple orthogonal methods (IFA, western blot, yeast two-hybrid, pull-down) in a single lab confirming expression, localization, and complex membership\",\n      \"pmids\": [\"24047207\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Interaction of SNRPD1 (PfSmD1) with PfSMN (survival of motor neuron, tudor domain-containing protein) is methylation-dependent, as shown by pull-down assays. PfPRMT5 (arginine methyltransferase) associates with SNRPD1 by co-immunoprecipitation, indicating arginine methylation of SNRPD1 (or its partners) is required for spliceosomal Sm core complex assembly in the cytoplasm.\",\n      \"method\": \"In vitro pull-down assays, co-immunoprecipitation, MALDI-TOF spectrometry\",\n      \"journal\": \"Malaria journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal pull-down and co-IP with mass spectrometry identification, single lab, two orthogonal methods\",\n      \"pmids\": [\"24047207\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"current_model\": \"In P. falciparum, SNRPD1 (PfSmD1/PF3D7_1125500) is a nucleo-cytoplasmic Sm-like protein that forms part of a heptameric spliceosomal core complex; its interaction with the Tudor-domain protein PfSMN is methylation-dependent, and it associates with the arginine methyltransferase PfPRMT5, implicating arginine methylation in cytoplasmic assembly of the Sm core complex.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"SNRPD1 (PfSmD1/PF3D7_1125500) is an Sm-class spliceosomal core protein of P. falciparum that assembles into a heptameric Sm core complex resembling, with a slightly altered subunit arrangement, the human spliceosomal Sm ring [#1]. It is expressed in asexual blood stages and displays nucleo-cytoplasmic localization, consistent with cytoplasmic Sm-core assembly followed by nuclear function [#1]. Its incorporation into this complex is governed by arginine methylation: SNRPD1 interacts with the Tudor-domain SMN protein PfSMN in a methylation-dependent manner and associates with the arginine methyltransferase PfPRMT5, implicating methylation-dependent recognition in cytoplasmic assembly of the Sm core [#2]. Beyond its membership in the Sm core complex and these methylation-dependent partner interactions, no further mechanistic detail about SNRPD1 has been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2010,\n      \"claim\": \"To place SNRPD1 within the parasite's RNA-processing machinery, an early interaction screen asked which proteins bind it, linking it to spliceosome assembly.\",\n      \"evidence\": \"Yeast two-hybrid screen identifying an interaction with the Tudor domain of PfTudor-SN in P. falciparum\",\n      \"pmids\": [\"20713134\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"Single yeast two-hybrid result with no orthogonal validation of the SNRPD1-specific interaction\",\n        \"Functional consequence of the PfTudor-SN interaction not tested\",\n        \"No demonstration that this interaction occurs in vivo in blood stages\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"To establish whether SNRPD1 is a bona fide Sm-core subunit, its expression, localization, and complex membership were characterized, defining a parasite heptameric Sm core complex.\",\n      \"evidence\": \"Immunofluorescence, western blotting, yeast two-hybrid, and in vitro pull-down assays in P. falciparum asexual blood stages\",\n      \"pmids\": [\"24047207\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Stoichiometry and exact subunit arrangement of the parasite complex not resolved structurally\",\n        \"Direct role of SNRPD1 in snRNP assembly or pre-mRNA splicing not functionally tested\",\n        \"No genetic knockdown/knockout to assess essentiality\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"To determine how Sm core assembly is regulated, the methylation dependence of SNRPD1's partner interactions was tested, implicating arginine methylation in cytoplasmic Sm-core assembly.\",\n      \"evidence\": \"In vitro pull-down, co-immunoprecipitation, and MALDI-TOF identification of methylation-dependent PfSMN binding and PfPRMT5 association in P. falciparum\",\n      \"pmids\": [\"24047207\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Direct arginine-methylated residues on SNRPD1 not mapped\",\n        \"Whether PfPRMT5 methylates SNRPD1 itself versus its partners not distinguished\",\n        \"In vivo requirement of methylation for splicing not established\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The functional role of SNRPD1 in pre-mRNA splicing and parasite viability, and the structural basis of the parasite Sm core, remain undefined.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No genetic loss-of-function data on SNRPD1 in any parasite stage\",\n        \"No structural model of the parasite Sm heptamer\",\n        \"No direct demonstration of SNRPD1 function in splicing\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [1]},\n      {\"term_id\": \"GO:0005737\", \"supporting_discovery_ids\": [1]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0000398\", \"supporting_discovery_ids\": [1]}\n    ],\n    \"complexes\": [\n      \"Heptameric spliceosomal Sm core complex\"\n    ],\n    \"partners\": [\n      \"PfTudor-SN (PfTu-TSN)\",\n      \"PfSMN (survival of motor neuron, Tudor-domain protein)\",\n      \"PfPRMT5 (arginine methyltransferase)\"\n    ],\n    \"other_free_text\": [\n      \"Interaction with PfSMN is methylation-dependent, implicating arginine methylation in cytoplasmic Sm-core assembly [#2]\",\n      \"Parasite Sm core complex subunit arrangement differs slightly from the human complex [#1]\"\n    ]\n  }\n}","audit_flag":{"gene":"PF3D7_1125500","tier":"IDENTITY_CHECK","verdict":"identity unverified","subtype":"names_other_cards","uniprot_band":"","rules_fired":"R12","issue":"No cited paper names this card; 2 of 2 cited papers name other catalogue genes (PF3D7_0617800, PF3D7_0323500, PF3D7_1361000). The summary may describe one of those genes."},"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_1125500","name":null,"product":"small nuclear ribonucleoprotein Sm D1, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_0922800","name":null,"product":"small nuclear ribonucleoprotein Sm D1, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_0923400","name":null,"product":"small nuclear ribonucleoprotein Sm D1, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"SNRPD1","evaluation":null}