{"gene":"PBANKA_API00430","run_date":"2026-09-07T10:55:51","timeline":{"discoveries":[{"year":2006,"finding":"In AZ-resistant P. falciparum lines, a G76V mutation was identified in the apicoplast-encoded ribosomal protein L4 (rpl4/PfRpl4). Molecular modeling of mutant PfRpl4 with azithromycin suggests that this mutation causes an altered orientation of the L75 side chain that could preclude azithromycin binding, implicating rpl4 as a component of the 50S ribosome polypeptide exit tunnel targeted by azithromycin in the apicoplast.","method":"Resistance selection in vitro, Sanger sequencing of resistant lines, molecular modeling of mutant protein with drug","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2/3 / Moderate — resistance selection with sequencing identifies functional mutation, molecular modeling supports mechanism, but no in vitro reconstitution or mutagenesis complementation performed; single lab","pmids":["17110371"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":"7G8"},{"species":"Plasmodium falciparum","strain":"Dd2"}]},{"year":2006,"finding":"rpl4/PfRpl4 is predicted to associate with the nuclear genome-encoded PfRpl22 and the large subunit rRNA to form the 50S ribosome polypeptide exit tunnel in the apicoplast. The rpl4 gene is apicoplast-encoded, and the polypeptide exit tunnel it forms is the target occupied by azithromycin.","method":"Structural modeling, sequence analysis, resistance selection","journal":"The Journal of biological chemistry","confidence":"Low","confidence_rationale":"Tier 4 / Weak — complex membership inferred from computational modeling and sequence homology only; no direct biochemical reconstitution of the complex","pmids":["17110371"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"current_model":"In Plasmodium falciparum, the apicoplast-encoded 50S ribosomal protein L4 (rpl4/PfRpl4) forms part of the polypeptide exit tunnel of the apicoplast 50S ribosome together with PfRpl22 and large subunit rRNA, and a G76V resistance mutation in rpl4 likely alters drug binding geometry to preclude azithromycin from occupying this tunnel."},"narrative":{"mechanistic_narrative":"PBANKA_API00430 (rpl4) is inferred, from evidence in Plasmodium falciparum, to encode an apicoplast-encoded 50S ribosomal protein L4 that contributes to the polypeptide exit tunnel of the apicoplast ribosome, the site targeted by azithromycin [PMID:17110371]. In azithromycin-resistant P. falciparum lines a G76V mutation in rpl4 was identified, and molecular modeling indicates this substitution reorients the neighboring L75 side chain in a way that would preclude azithromycin from occupying the exit tunnel, implicating rpl4 directly in the drug-binding architecture of the apicoplast 50S ribosome [PMID:17110371]. Beyond this resistance-mapping and modeling evidence — including the computationally inferred association of rpl4 with PfRpl22 and large-subunit rRNA to form the exit tunnel [PMID:17110371] — no direct biochemical characterization of rpl4 has been established in the available corpus, and all findings derive from P. falciparum rather than the subject P. berghei gene itself.","teleology":[{"year":2006,"claim":"Whether azithromycin acts on the apicoplast translation machinery was addressed by mapping resistance to a specific ribosomal protein, establishing rpl4 as part of the drug's target.","evidence":"In vitro resistance selection with Sanger sequencing of resistant P. falciparum lines plus molecular modeling of mutant PfRpl4 with azithromycin","pmids":["17110371"],"confidence":"Medium","gaps":["No mutagenesis complementation or in vitro reconstitution confirms G76V is causative for resistance","The modeled altered L75 orientation is not experimentally validated by structure","Findings are in P. falciparum; the P. berghei ortholog PBANKA_API00430 was not directly tested"],"attribution":[{"species":"Plasmodium falciparum","strain":"7G8"},{"species":"Plasmodium falciparum","strain":"Dd2"}]},{"year":2006,"claim":"The structural context of rpl4 was addressed by predicting its assembly with PfRpl22 and large-subunit rRNA into the 50S polypeptide exit tunnel, framing rpl4 as a tunnel-forming component rather than a standalone drug target.","evidence":"Structural modeling and sequence analysis in P. falciparum","pmids":["17110371"],"confidence":"Low","gaps":["Complex membership is inferred from computational modeling and homology only, with no biochemical reconstitution","Direct interaction between rpl4 and PfRpl22 or rRNA is not demonstrated","No evidence addresses complex assembly for PBANKA_API00430 itself"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":null,"claim":"Whether PBANKA_API00430 in P. berghei forms the apicoplast 50S exit tunnel, binds azithromycin, and carries the same resistance liability remains uncharacterized in the available corpus.","evidence":"No direct experimental study of the subject gene is present in the timeline","pmids":[],"confidence":"Low","gaps":["No direct functional, biochemical, or genetic data on PBANKA_API00430","No experimental validation of exit-tunnel assembly or drug binding in any species","No structural determination of the apicoplast 50S ribosome"],"attribution":[]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["Apicoplast 50S ribosomal large subunit polypeptide exit tunnel (inferred, with PfRpl22 and large-subunit rRNA) [#1]"],"partners":["PFRPL22 (PREDICTED, COMPUTATIONAL) [#1]","LARGE SUBUNIT RRNA (PREDICTED, COMPUTATIONAL) [#1]"],"other_free_text":["G76V mutation in rpl4 associated with azithromycin resistance in P. falciparum [#0]","All evidence derives from P. falciparum; no direct data on the subject P. berghei gene PBANKA_API00430"]}},"prefetch_data":{},"corpus_meta":[{"pmid":"17110371","id":"PMC_17110371","title":"In vitro efficacy, resistance selection, and structural modeling studies implicate the malarial parasite apicoplast as the target of azithromycin.","date":"2006","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/17110371","citation_count":126,"is_preprint":false,"source_species":["Pb"],"role":"primary","match_terms":["Pfrpl4"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":3474,"output_tokens":706,"usd":0.010506,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5355,"output_tokens":1688,"usd":0.034487,"stage2_stop_reason":"end_turn"},"total_usd":0.044993,"stage1_batch_id":"msgbatch_01DbiymDmubkPpYvdbAu5a7V","stage2_batch_id":"msgbatch_012TbrWvMRH129T7PQ4SmvrJ","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2006,\n      \"finding\": \"In AZ-resistant P. falciparum lines, a G76V mutation was identified in the apicoplast-encoded ribosomal protein L4 (rpl4/PfRpl4). Molecular modeling of mutant PfRpl4 with azithromycin suggests that this mutation causes an altered orientation of the L75 side chain that could preclude azithromycin binding, implicating rpl4 as a component of the 50S ribosome polypeptide exit tunnel targeted by azithromycin in the apicoplast.\",\n      \"method\": \"Resistance selection in vitro, Sanger sequencing of resistant lines, molecular modeling of mutant protein with drug\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2/3 / Moderate — resistance selection with sequencing identifies functional mutation, molecular modeling supports mechanism, but no in vitro reconstitution or mutagenesis complementation performed; single lab\",\n      \"pmids\": [\"17110371\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"7G8\"},\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"Dd2\"}\n      ]\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"rpl4/PfRpl4 is predicted to associate with the nuclear genome-encoded PfRpl22 and the large subunit rRNA to form the 50S ribosome polypeptide exit tunnel in the apicoplast. The rpl4 gene is apicoplast-encoded, and the polypeptide exit tunnel it forms is the target occupied by azithromycin.\",\n      \"method\": \"Structural modeling, sequence analysis, resistance selection\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 4 / Weak — complex membership inferred from computational modeling and sequence homology only; no direct biochemical reconstitution of the complex\",\n      \"pmids\": [\"17110371\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"current_model\": \"In Plasmodium falciparum, the apicoplast-encoded 50S ribosomal protein L4 (rpl4/PfRpl4) forms part of the polypeptide exit tunnel of the apicoplast 50S ribosome together with PfRpl22 and large subunit rRNA, and a G76V resistance mutation in rpl4 likely alters drug binding geometry to preclude azithromycin from occupying this tunnel.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PBANKA_API00430 (rpl4) is inferred, from evidence in Plasmodium falciparum, to encode an apicoplast-encoded 50S ribosomal protein L4 that contributes to the polypeptide exit tunnel of the apicoplast ribosome, the site targeted by azithromycin [#0]. In azithromycin-resistant P. falciparum lines a G76V mutation in rpl4 was identified, and molecular modeling indicates this substitution reorients the neighboring L75 side chain in a way that would preclude azithromycin from occupying the exit tunnel, implicating rpl4 directly in the drug-binding architecture of the apicoplast 50S ribosome [#0]. Beyond this resistance-mapping and modeling evidence — including the computationally inferred association of rpl4 with PfRpl22 and large-subunit rRNA to form the exit tunnel [#1] — no direct biochemical characterization of rpl4 has been established in the available corpus, and all findings derive from P. falciparum rather than the subject P. berghei gene itself.\",\n  \"teleology\": [\n    {\n      \"year\": 2006,\n      \"claim\": \"Whether azithromycin acts on the apicoplast translation machinery was addressed by mapping resistance to a specific ribosomal protein, establishing rpl4 as part of the drug's target.\",\n      \"evidence\": \"In vitro resistance selection with Sanger sequencing of resistant P. falciparum lines plus molecular modeling of mutant PfRpl4 with azithromycin\",\n      \"pmids\": [\"17110371\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No mutagenesis complementation or in vitro reconstitution confirms G76V is causative for resistance\",\n        \"The modeled altered L75 orientation is not experimentally validated by structure\",\n        \"Findings are in P. falciparum; the P. berghei ortholog PBANKA_API00430 was not directly tested\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"7G8\"},\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"Dd2\"}\n      ]\n    },\n    {\n      \"year\": 2006,\n      \"claim\": \"The structural context of rpl4 was addressed by predicting its assembly with PfRpl22 and large-subunit rRNA into the 50S polypeptide exit tunnel, framing rpl4 as a tunnel-forming component rather than a standalone drug target.\",\n      \"evidence\": \"Structural modeling and sequence analysis in P. falciparum\",\n      \"pmids\": [\"17110371\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"Complex membership is inferred from computational modeling and homology only, with no biochemical reconstitution\",\n        \"Direct interaction between rpl4 and PfRpl22 or rRNA is not demonstrated\",\n        \"No evidence addresses complex assembly for PBANKA_API00430 itself\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Whether PBANKA_API00430 in P. berghei forms the apicoplast 50S exit tunnel, binds azithromycin, and carries the same resistance liability remains uncharacterized in the available corpus.\",\n      \"evidence\": \"No direct experimental study of the subject gene is present in the timeline\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No direct functional, biochemical, or genetic data on PBANKA_API00430\",\n        \"No experimental validation of exit-tunnel assembly or drug binding in any species\",\n        \"No structural determination of the apicoplast 50S ribosome\"\n      ],\n      \"attribution\": []\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003735\", \"supporting_discovery_ids\": [0, 1]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0009536\", \"supporting_discovery_ids\": [0, 1]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0006412\", \"supporting_discovery_ids\": [0, 1]}\n    ],\n    \"complexes\": [\n      \"Apicoplast 50S ribosomal large subunit polypeptide exit tunnel (inferred, with PfRpl22 and large-subunit rRNA) [#1]\"\n    ],\n    \"partners\": [\n      \"PfRpl22 (predicted, computational) [#1]\",\n      \"Large subunit rRNA (predicted, computational) [#1]\"\n    ],\n    \"other_free_text\": [\n      \"G76V mutation in rpl4 associated with azithromycin resistance in P. falciparum [#0]\",\n      \"All evidence derives from P. falciparum; no direct data on the subject P. berghei gene PBANKA_API00430\"\n    ]\n  }\n}","audit_flag":{"gene":"PBANKA_API00430","tier":"IDENTITY_CHECK","verdict":"identity unverified","subtype":"names_other_cards","uniprot_band":"","rules_fired":"R12","issue":"No cited paper names this card; 1 of 1 cited papers name other catalogue genes (PF3D7_0507100, PF3D7_1467400). The summary may describe one of those genes."},"strains":[{"strain":"PbANKA","gene_id":"PBANKA_API00430","name":null,"product":"50S ribosomal protein L4, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"rpl4","evaluation":null}