{"gene":"PF3D7_0705700","run_date":"2026-09-08T12:51:27","timeline":{"discoveries":[{"year":2014,"finding":"The cryo-EM structure of the P. falciparum 80S ribosome at 3.2 Å resolution was solved, placing the 40S small subunit proteins (including S29/PF3D7_0705700 as a constituent of the small subunit) in their structural context. The structure established that emetine binds the E-site of the ribosomal small subunit and blocks mRNA/tRNA translocation.","method":"Cryo-EM structure determination at 3.2 Å resolution of the P. falciparum 80S ribosome bound to emetine","journal":"eLife","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — atomic-resolution cryo-EM structure of the full ribosome; S29/PF3D7_0705700 is a subunit constituent but no specific functional experiment was performed on it individually; its membership in the small subunit complex is established structurally in a single study","pmids":["24913268"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2015,"finding":"Five cryo-EM reconstructions of ribosomes purified from P. falciparum blood-stage schizonts at sub-nanometer resolution were obtained, and atomic models were built by flexible fitting, placing S29/PF3D7_0705700 as a structural component of the 40S small subunit in multiple translational states. Structural and dynamic features differentiating the P. falciparum ribosome from mammalian ribosomes were identified.","method":"Cryo-EM with multiple reconstructions and flexible-fitting atomic model building of ribosomes purified from P. falciparum schizonts","journal":"Nucleic acids research","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — sub-nanometer cryo-EM with atomic model building from a single lab; S29/PF3D7_0705700 is established as a small-subunit constituent but no experiment targeted it specifically","pmids":["26432834"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2025,"finding":"Eight high-resolution in situ cryo-electron tomography structures of the native malarial ribosome in actively translating states were determined inside P. falciparum-infected erythrocytes, further establishing the structural context of the 40S small subunit (of which S29/PF3D7_0705700 is a component) during the translation elongation cycle in the native cellular environment.","method":"In situ cryo-electron tomography of P. falciparum-infected erythrocytes; integrated structural biology approach","journal":"Nature structural & molecular biology","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — highest-resolution in situ structural study of the native ribosome in a single publication; S29/PF3D7_0705700 is a structural constituent but was not individually interrogated","pmids":["40825879"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"current_model":"PF3D7_0705700 (S29) is established as a structural constituent of the P. falciparum 40S ribosomal small subunit, its position defined by multiple cryo-EM and cryo-ET structures of the Pf80S ribosome at near-atomic resolution, but no experiment has directly interrogated its individual function, binding partners, or post-translational modifications."},"narrative":{"mechanistic_narrative":"PF3D7_0705700 (S29) is a structural constituent of the 40S small subunit of the Plasmodium falciparum 80S ribosome, placed in its structural context by cryo-EM of the intact ribosome at 3.2 Å resolution [PMID:24913268] and by multiple reconstructions of ribosomes purified from blood-stage schizonts that resolved distinct translational states and features distinguishing the parasite ribosome from mammalian ribosomes [PMID:26432834]. In situ cryo-electron tomography of the native ribosome inside infected erythrocytes has further situated the 40S subunit, and thereby S29, within actively translating states of the elongation cycle [PMID:40825879]. Beyond its assignment as a small-subunit component in these structures, no experiment in the available corpus has directly interrogated the individual function, binding partners, or post-translational modifications of PF3D7_0705700; the corpus establishes only its membership in the 40S small subunit.","teleology":[{"year":2014,"claim":"The first atomic-resolution structure of the P. falciparum 80S ribosome was needed to place small-subunit proteins in structural context and to understand small-molecule inhibition; this established S29 as a resolved constituent of the 40S small subunit.","evidence":"Cryo-EM at 3.2 Å of the P. falciparum 80S ribosome bound to emetine","pmids":["24913268"],"confidence":"Medium","gaps":["No functional experiment targeted S29 individually","Binding partners of S29 beyond the ribosome not defined","No post-translational modification data"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2015,"claim":"To capture the parasite ribosome across functional states, multiple reconstructions from schizont-purified ribosomes resolved S29 as a small-subunit component in several translational conformations and identified features distinguishing the parasite from the mammalian ribosome.","evidence":"Cryo-EM with multiple reconstructions and flexible-fitting atomic model building of ribosomes from P. falciparum schizonts","pmids":["26432834"],"confidence":"Medium","gaps":["Structural placement only; no assay of S29-specific contribution to translation","Species-specific features not attributed to S29 in particular"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2025,"claim":"Whether the ribosome's structural arrangement seen in purified samples holds in the native cell was addressed by in situ tomography, situating the 40S subunit, and S29, within actively translating states inside infected erythrocytes.","evidence":"In situ cryo-electron tomography of P. falciparum-infected erythrocytes","pmids":["40825879"],"confidence":"Medium","gaps":["S29 not individually interrogated","No mechanistic role assigned to S29 within elongation","No interaction or modification data"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":null,"claim":"The individual function, binding partners, post-translational modifications, and essentiality of PF3D7_0705700 beyond its structural membership in the 40S small subunit remain uncharacterized in the available corpus.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No gene-specific knockdown, knockout, or complementation for S29","No S29-specific interactome","No evidence for extraribosomal or moonlighting roles"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["40S small ribosomal subunit of the P. falciparum 80S ribosome"],"partners":[],"other_free_text":["S29/PF3D7_0705700 is established only as a structural constituent of the 40S small subunit; no individual function, binding partner, or post-translational modification has been experimentally interrogated in the available corpus.","Structural studies resolve S29 within the parasite ribosome across multiple translational states, including in situ within infected erythrocytes [#0, #1, #2]."]}},"prefetch_data":{},"corpus_meta":[{"pmid":"24913268","id":"PMC_24913268","title":"Cryo-EM structure of the Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine.","date":"2014","source":"eLife","url":"https://pubmed.ncbi.nlm.nih.gov/24913268","citation_count":276,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["curated_ref"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"26432834","id":"PMC_26432834","title":"Dynamical features of the Plasmodium falciparum ribosome during translation.","date":"2015","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/26432834","citation_count":46,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["curated_ref"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"40825879","id":"PMC_40825879","title":"Integrated structural biology of the native malarial translation machinery and its inhibition by an antimalarial drug.","date":"2025","source":"Nature structural & molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/40825879","citation_count":10,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["curated_ref"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"34998927","id":"PMC_34998927","title":"Plasmodium falciparum Cysteine Rich Secretory Protein uniquely localizes to one end of male gametes.","date":"2022","source":"Molecular and biochemical parasitology","url":"https://pubmed.ncbi.nlm.nih.gov/34998927","citation_count":4,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["CRISP","cysteine-rich secretory protein"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"40480224","id":"PMC_40480224","title":"Antimalarial drug artemisinin stabilizes PfRACK1 binding to the ribosome.","date":"2025","source":"Structure (London, England : 1993)","url":"https://pubmed.ncbi.nlm.nih.gov/40480224","citation_count":4,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["curated_ref"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":4851,"output_tokens":1001,"usd":0.014784,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5714,"output_tokens":1681,"usd":0.035298,"stage2_stop_reason":"end_turn"},"total_usd":0.050082,"stage1_batch_id":"msgbatch_01DisAaTypwmC8QwdMBuePHo","stage2_batch_id":"msgbatch_0184zxZTqxiEfdYYfPMfkqjb","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2014,\n      \"finding\": \"The cryo-EM structure of the P. falciparum 80S ribosome at 3.2 Å resolution was solved, placing the 40S small subunit proteins (including S29/PF3D7_0705700 as a constituent of the small subunit) in their structural context. The structure established that emetine binds the E-site of the ribosomal small subunit and blocks mRNA/tRNA translocation.\",\n      \"method\": \"Cryo-EM structure determination at 3.2 Å resolution of the P. falciparum 80S ribosome bound to emetine\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — atomic-resolution cryo-EM structure of the full ribosome; S29/PF3D7_0705700 is a subunit constituent but no specific functional experiment was performed on it individually; its membership in the small subunit complex is established structurally in a single study\",\n      \"pmids\": [\"24913268\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Five cryo-EM reconstructions of ribosomes purified from P. falciparum blood-stage schizonts at sub-nanometer resolution were obtained, and atomic models were built by flexible fitting, placing S29/PF3D7_0705700 as a structural component of the 40S small subunit in multiple translational states. Structural and dynamic features differentiating the P. falciparum ribosome from mammalian ribosomes were identified.\",\n      \"method\": \"Cryo-EM with multiple reconstructions and flexible-fitting atomic model building of ribosomes purified from P. falciparum schizonts\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — sub-nanometer cryo-EM with atomic model building from a single lab; S29/PF3D7_0705700 is established as a small-subunit constituent but no experiment targeted it specifically\",\n      \"pmids\": [\"26432834\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Eight high-resolution in situ cryo-electron tomography structures of the native malarial ribosome in actively translating states were determined inside P. falciparum-infected erythrocytes, further establishing the structural context of the 40S small subunit (of which S29/PF3D7_0705700 is a component) during the translation elongation cycle in the native cellular environment.\",\n      \"method\": \"In situ cryo-electron tomography of P. falciparum-infected erythrocytes; integrated structural biology approach\",\n      \"journal\": \"Nature structural & molecular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — highest-resolution in situ structural study of the native ribosome in a single publication; S29/PF3D7_0705700 is a structural constituent but was not individually interrogated\",\n      \"pmids\": [\"40825879\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"current_model\": \"PF3D7_0705700 (S29) is established as a structural constituent of the P. falciparum 40S ribosomal small subunit, its position defined by multiple cryo-EM and cryo-ET structures of the Pf80S ribosome at near-atomic resolution, but no experiment has directly interrogated its individual function, binding partners, or post-translational modifications.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PF3D7_0705700 (S29) is a structural constituent of the 40S small subunit of the Plasmodium falciparum 80S ribosome, placed in its structural context by cryo-EM of the intact ribosome at 3.2 Å resolution [#0] and by multiple reconstructions of ribosomes purified from blood-stage schizonts that resolved distinct translational states and features distinguishing the parasite ribosome from mammalian ribosomes [#1]. In situ cryo-electron tomography of the native ribosome inside infected erythrocytes has further situated the 40S subunit, and thereby S29, within actively translating states of the elongation cycle [#2]. Beyond its assignment as a small-subunit component in these structures, no experiment in the available corpus has directly interrogated the individual function, binding partners, or post-translational modifications of PF3D7_0705700; the corpus establishes only its membership in the 40S small subunit.\",\n  \"teleology\": [\n    {\n      \"year\": 2014,\n      \"claim\": \"The first atomic-resolution structure of the P. falciparum 80S ribosome was needed to place small-subunit proteins in structural context and to understand small-molecule inhibition; this established S29 as a resolved constituent of the 40S small subunit.\",\n      \"evidence\": \"Cryo-EM at 3.2 Å of the P. falciparum 80S ribosome bound to emetine\",\n      \"pmids\": [\"24913268\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No functional experiment targeted S29 individually\", \"Binding partners of S29 beyond the ribosome not defined\", \"No post-translational modification data\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"To capture the parasite ribosome across functional states, multiple reconstructions from schizont-purified ribosomes resolved S29 as a small-subunit component in several translational conformations and identified features distinguishing the parasite from the mammalian ribosome.\",\n      \"evidence\": \"Cryo-EM with multiple reconstructions and flexible-fitting atomic model building of ribosomes from P. falciparum schizonts\",\n      \"pmids\": [\"26432834\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Structural placement only; no assay of S29-specific contribution to translation\", \"Species-specific features not attributed to S29 in particular\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Whether the ribosome's structural arrangement seen in purified samples holds in the native cell was addressed by in situ tomography, situating the 40S subunit, and S29, within actively translating states inside infected erythrocytes.\",\n      \"evidence\": \"In situ cryo-electron tomography of P. falciparum-infected erythrocytes\",\n      \"pmids\": [\"40825879\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"S29 not individually interrogated\", \"No mechanistic role assigned to S29 within elongation\", \"No interaction or modification data\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The individual function, binding partners, post-translational modifications, and essentiality of PF3D7_0705700 beyond its structural membership in the 40S small subunit remain uncharacterized in the available corpus.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No gene-specific knockdown, knockout, or complementation for S29\", \"No S29-specific interactome\", \"No evidence for extraribosomal or moonlighting roles\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003735\", \"supporting_discovery_ids\": [0, 1, 2]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0022627\", \"supporting_discovery_ids\": [0, 1, 2]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0006412\", \"supporting_discovery_ids\": [0, 1, 2]}\n    ],\n    \"complexes\": [\"40S small ribosomal subunit of the P. falciparum 80S ribosome\"],\n    \"partners\": [],\n    \"other_free_text\": [\n      \"S29/PF3D7_0705700 is established only as a structural constituent of the 40S small subunit; no individual function, binding partner, or post-translational modification has been experimentally interrogated in the available corpus.\",\n      \"Structural studies resolve S29 within the parasite ribosome across multiple translational states, including in situ within infected erythrocytes [#0, #1, #2].\"\n    ]\n  }\n}","audit_flag":null,"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_0705700","name":null,"product":"40S ribosomal protein S29, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"Pf3D7","gene_id":"PF3D7_0705800","name":null,"product":"cysteine-rich secretory protein","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_0803400","name":null,"product":"40S ribosomal protein S29, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_0104200","name":null,"product":"40S ribosomal protein S29, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_0104300","name":null,"product":"cysteine-rich secretory protein, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"CRISP","evaluation":null}