{"gene":"PF3D7_1302800","run_date":"2026-09-08T14:19:06","timeline":{"discoveries":[{"year":2014,"finding":"Cryo-EM structure of the P. falciparum 80S ribosome at 3.2 Å resolution revealed the small subunit (40S), of which S7/PF3D7_1302800 is a component, bound to emetine at the E-site; emetine blocks mRNA/tRNA translocation by interacting with the ribosomal small subunit E-site, sharing a binding site with pactamycin.","method":"Cryo-EM structure determination at 3.2 Å resolution","journal":"eLife","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — high-resolution cryo-EM structure of the intact ribosome complex, but PF3D7_1302800 itself is not individually characterized beyond being a structural component of the 40S subunit","pmids":["24913268"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2023,"finding":"Ribosome heterogeneity in Plasmodium parasites was characterized, implicating 40S ribosomal proteins including S7/PF3D7_1302800 as structural components of stage-specific ribosome variants across the parasite life cycle.","method":"Structural and comparative genomic analysis of ribosome composition across life-cycle stages","journal":"PLoS pathogens","confidence":"Low","confidence_rationale":"Tier 3 / Weak — abstract only hints at ribosome heterogeneity without providing specific mechanistic data on PF3D7_1302800 individually","pmids":["37053161"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2025,"finding":"In situ cryo-electron tomography of P. falciparum-infected erythrocytes resolved eight high-resolution structures of the native malarial ribosome in actively translating states, establishing the structural context of the 40S subunit (of which S7/PF3D7_1302800 is a component) during elongation; treatment with a Plasmodium-specific translation inhibitor decreased elongation factor-bound ribosomal states and apparently upregulated ribosome biogenesis.","method":"In situ cryo-electron tomography at high resolution inside infected erythrocytes","journal":"Nature structural & molecular biology","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — rigorous in situ structural method, but PF3D7_1302800 is not individually interrogated; findings pertain to the ribosome complex as a whole","pmids":["40825879"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"current_model":"PF3D7_1302800 (S7) is established as a structural component of the P. falciparum 40S ribosomal small subunit, which participates in mRNA/tRNA translocation during translation elongation and is the target of drugs such as emetine and mefloquine that bind the small subunit; no experiment has individually characterized the molecular function or interactions of PF3D7_1302800 itself beyond its membership in the 40S subunit."},"narrative":{"mechanistic_narrative":"PF3D7_1302800 (S7) is a structural component of the small (40S) subunit of the P. falciparum 80S ribosome, resolved within cryo-EM structures of the intact parasite ribosome [PMID:24913268]. In this context the 40S subunit binds the translation inhibitor emetine at the E-site, where the drug blocks mRNA/tRNA translocation, sharing a binding site with pactamycin [PMID:24913268]. The 40S subunit that contains S7 is present in stage-specific ribosome variants across the parasite life cycle [PMID:37053161] and has been captured in actively translating, elongation-factor-bound states inside infected erythrocytes by in situ cryo-electron tomography [PMID:40825879]. Beyond its membership in the 40S small subunit and the structural roles inferred from that context, no experiment in the available corpus has individually characterized the molecular function or interactions of PF3D7_1302800 itself.","teleology":[{"year":2014,"claim":"Establishing the atomic architecture of the P. falciparum ribosome placed S7 within the 40S small subunit and defined the E-site as the binding pocket where emetine arrests mRNA/tRNA translocation, framing the subunit as an antimalarial drug target.","evidence":"Cryo-EM structure of the P. falciparum 80S ribosome at 3.2 Å resolution with bound emetine","pmids":["24913268"],"confidence":"Medium","gaps":["PF3D7_1302800 is not individually interrogated; its specific contacts and function within the subunit are not resolved","No direct evidence that S7 itself contacts the emetine-binding E-site","No functional assay tying S7 to translocation"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2023,"claim":"Comparative analysis of ribosome composition across life-cycle stages raised the question of whether the parasite deploys distinct ribosome variants, implicating 40S proteins including S7 as components of stage-specific assemblies.","evidence":"Structural and comparative genomic analysis of ribosome heterogeneity across P. falciparum life-cycle stages","pmids":["37053161"],"confidence":"Low","gaps":["Abstract-level evidence only; no mechanistic data specific to PF3D7_1302800","Whether S7 itself varies between stage-specific variants is not shown","Functional consequence of any heterogeneity for S7 is unaddressed"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2025,"claim":"Resolving native ribosomes inside infected erythrocytes established the structural context of the 40S subunit during active elongation and showed that a Plasmodium-specific inhibitor shifts the balance of translating versus biogenesis states.","evidence":"In situ cryo-electron tomography of P. falciparum-infected erythrocytes yielding eight high-resolution translating-ribosome structures","pmids":["40825879"],"confidence":"Medium","gaps":["S7 is not individually interrogated; findings pertain to the whole ribosome","No S7-specific role in the elongation-to-biogenesis shift is demonstrated"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":null,"claim":"Whether PF3D7_1302800 has any function, interaction, or phenotype distinct from its structural membership in the 40S subunit remains uncharacterized.","evidence":"No discovery in the corpus interrogates PF3D7_1302800 individually","pmids":[],"confidence":"Low","gaps":["No genetic knockdown/knockout of S7 reported","No S7-specific interaction partners beyond the 40S subunit identified","No assembly or extraribosomal function tested"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["40S ribosomal small subunit (P. falciparum)","80S ribosome (P. falciparum)"],"partners":[],"other_free_text":["S7 sits within the 40S subunit whose E-site binds the translation inhibitor emetine (shared site with pactamycin) [#0]","S7-containing 40S subunits are found in stage-specific ribosome variants across the P. falciparum life cycle [#1]","S7-containing ribosomes captured in actively translating, elongation-factor-bound states in situ; a Plasmodium-specific inhibitor shifted states toward ribosome biogenesis [#2]","No experiment individually characterizes PF3D7_1302800 beyond its membership in the 40S subunit"]}},"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":272,"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":45,"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":7,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["curated_ref"],"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":3,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["curated_ref"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"28288098","id":"PMC_28288098","title":"Mefloquine targets the Plasmodium falciparum 80S ribosome to inhibit protein synthesis.","date":"2017","source":"Nature 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microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/28540920","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"citation_expansion","match_terms":["fwd_cite"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":7152,"output_tokens":919,"usd":0.017621,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5610,"output_tokens":1936,"usd":0.038225,"stage2_stop_reason":"end_turn"},"total_usd":0.055846,"stage1_batch_id":"msgbatch_011BPjN2BL33F8cJXD1r7V7T","stage2_batch_id":"msgbatch_01Qwg6vP7qxkpL6Gsc7tajsb","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2014,\n      \"finding\": \"Cryo-EM structure of the P. falciparum 80S ribosome at 3.2 Å resolution revealed the small subunit (40S), of which S7/PF3D7_1302800 is a component, bound to emetine at the E-site; emetine blocks mRNA/tRNA translocation by interacting with the ribosomal small subunit E-site, sharing a binding site with pactamycin.\",\n      \"method\": \"Cryo-EM structure determination at 3.2 Å resolution\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — high-resolution cryo-EM structure of the intact ribosome complex, but PF3D7_1302800 itself is not individually characterized beyond being a structural component of the 40S subunit\",\n      \"pmids\": [\"24913268\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Ribosome heterogeneity in Plasmodium parasites was characterized, implicating 40S ribosomal proteins including S7/PF3D7_1302800 as structural components of stage-specific ribosome variants across the parasite life cycle.\",\n      \"method\": \"Structural and comparative genomic analysis of ribosome composition across life-cycle stages\",\n      \"journal\": \"PLoS pathogens\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — abstract only hints at ribosome heterogeneity without providing specific mechanistic data on PF3D7_1302800 individually\",\n      \"pmids\": [\"37053161\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"In situ cryo-electron tomography of P. falciparum-infected erythrocytes resolved eight high-resolution structures of the native malarial ribosome in actively translating states, establishing the structural context of the 40S subunit (of which S7/PF3D7_1302800 is a component) during elongation; treatment with a Plasmodium-specific translation inhibitor decreased elongation factor-bound ribosomal states and apparently upregulated ribosome biogenesis.\",\n      \"method\": \"In situ cryo-electron tomography at high resolution inside infected erythrocytes\",\n      \"journal\": \"Nature structural & molecular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — rigorous in situ structural method, but PF3D7_1302800 is not individually interrogated; findings pertain to the ribosome complex as a whole\",\n      \"pmids\": [\"40825879\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"current_model\": \"PF3D7_1302800 (S7) is established as a structural component of the P. falciparum 40S ribosomal small subunit, which participates in mRNA/tRNA translocation during translation elongation and is the target of drugs such as emetine and mefloquine that bind the small subunit; no experiment has individually characterized the molecular function or interactions of PF3D7_1302800 itself beyond its membership in the 40S subunit.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PF3D7_1302800 (S7) is a structural component of the small (40S) subunit of the P. falciparum 80S ribosome, resolved within cryo-EM structures of the intact parasite ribosome [#0]. In this context the 40S subunit binds the translation inhibitor emetine at the E-site, where the drug blocks mRNA/tRNA translocation, sharing a binding site with pactamycin [#0]. The 40S subunit that contains S7 is present in stage-specific ribosome variants across the parasite life cycle [#1] and has been captured in actively translating, elongation-factor-bound states inside infected erythrocytes by in situ cryo-electron tomography [#2]. Beyond its membership in the 40S small subunit and the structural roles inferred from that context, no experiment in the available corpus has individually characterized the molecular function or interactions of PF3D7_1302800 itself.\",\n  \"teleology\": [\n    {\n      \"year\": 2014,\n      \"claim\": \"Establishing the atomic architecture of the P. falciparum ribosome placed S7 within the 40S small subunit and defined the E-site as the binding pocket where emetine arrests mRNA/tRNA translocation, framing the subunit as an antimalarial drug target.\",\n      \"evidence\": \"Cryo-EM structure of the P. falciparum 80S ribosome at 3.2 \\u00c5 resolution with bound emetine\",\n      \"pmids\": [\"24913268\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"PF3D7_1302800 is not individually interrogated; its specific contacts and function within the subunit are not resolved\",\n        \"No direct evidence that S7 itself contacts the emetine-binding E-site\",\n        \"No functional assay tying S7 to translocation\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Comparative analysis of ribosome composition across life-cycle stages raised the question of whether the parasite deploys distinct ribosome variants, implicating 40S proteins including S7 as components of stage-specific assemblies.\",\n      \"evidence\": \"Structural and comparative genomic analysis of ribosome heterogeneity across P. falciparum life-cycle stages\",\n      \"pmids\": [\"37053161\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"Abstract-level evidence only; no mechanistic data specific to PF3D7_1302800\",\n        \"Whether S7 itself varies between stage-specific variants is not shown\",\n        \"Functional consequence of any heterogeneity for S7 is unaddressed\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Resolving native ribosomes inside infected erythrocytes established the structural context of the 40S subunit during active elongation and showed that a Plasmodium-specific inhibitor shifts the balance of translating versus biogenesis states.\",\n      \"evidence\": \"In situ cryo-electron tomography of P. falciparum-infected erythrocytes yielding eight high-resolution translating-ribosome structures\",\n      \"pmids\": [\"40825879\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"S7 is not individually interrogated; findings pertain to the whole ribosome\",\n        \"No S7-specific role in the elongation-to-biogenesis shift is demonstrated\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Whether PF3D7_1302800 has any function, interaction, or phenotype distinct from its structural membership in the 40S subunit remains uncharacterized.\",\n      \"evidence\": \"No discovery in the corpus interrogates PF3D7_1302800 individually\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No genetic knockdown/knockout of S7 reported\",\n        \"No S7-specific interaction partners beyond the 40S subunit identified\",\n        \"No assembly or extraribosomal function tested\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\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:0006414\", \"supporting_discovery_ids\": [0, 2]}\n    ],\n    \"complexes\": [\n      \"40S ribosomal small subunit (P. falciparum)\",\n      \"80S ribosome (P. falciparum)\"\n    ],\n    \"partners\": [],\n    \"other_free_text\": [\n      \"S7 sits within the 40S subunit whose E-site binds the translation inhibitor emetine (shared site with pactamycin) [#0]\",\n      \"S7-containing 40S subunits are found in stage-specific ribosome variants across the P. falciparum life cycle [#1]\",\n      \"S7-containing ribosomes captured in actively translating, elongation-factor-bound states in situ; a Plasmodium-specific inhibitor shifted states toward ribosome biogenesis [#2]\",\n      \"No experiment individually characterizes PF3D7_1302800 beyond its membership in the 40S subunit\"\n    ]\n  }\n}","audit_flag":null,"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_1302800","name":null,"product":"40S ribosomal protein S7, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_1401300","name":null,"product":"40S ribosomal protein S7, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_1403000","name":null,"product":"40S ribosomal protein S7, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"","evaluation":null}