{"gene":"PF3D7_1008800","run_date":"2026-09-08T16:26:55","timeline":{"discoveries":[{"year":2012,"finding":"NOP5 (PF3D7_1008800/PF10_0085) was detected in the nuclear proteome of P. falciparum by high-accuracy mass spectrometry, and is noted as one of only three proteins previously localized to the parasite nucleolus.","method":"Organellar proteomics (high-accuracy mass spectrometry of isolated nuclei)","journal":"Genome biology","confidence":"Low","confidence_rationale":"Tier 3 / Weak — mass spectrometry detection in a pan-nuclear proteome catalog; no functional experiment performed on NOP5 itself in this paper","pmids":["23181666"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2018,"finding":"NOP5 (PF3D7_1008800) was enriched in DNA pull-downs using oligonucleotide probes containing de novo regulatory motif 028, together with the transcription factor AP2-I and chromatin-related factors (bromodomain proteins, HMGB3, SWIB/MDM2 domain protein), suggesting NOP5 associates with this regulatory DNA motif complex in P. falciparum intraerythrocytic stages.","method":"DNA oligonucleotide pull-down followed by mass spectrometry","journal":"Cell host & microbe","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single pull-down experiment in a large-scale study; no functional follow-up specific to NOP5","pmids":["29649445"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"current_model":"NOP5 (PF3D7_1008800) is a nucleolar protein in P. falciparum detected in the nuclear proteome by mass spectrometry, and has been found associated with a regulatory DNA motif complex containing the transcription factor AP2-I and chromatin factors in pull-down experiments; no direct enzymatic activity, structure, or functional mechanism has been established for this protein."},"narrative":{"mechanistic_narrative":"NOP5 (PF3D7_1008800) is a putative nucleolar protein of Plasmodium falciparum whose function has not been directly characterized in the available corpus. It was detected in the parasite nuclear proteome by high-accuracy mass spectrometry and is noted as one of only three proteins previously localized to the parasite nucleolus [PMID:23181666]. In DNA oligonucleotide pull-downs using probes bearing the de novo regulatory motif 028, NOP5 co-enriched with the transcription factor AP2-I and chromatin-associated factors (bromodomain proteins, HMGB3, and a SWIB/MDM2 domain protein), placing it in physical association with a regulatory DNA motif complex during intraerythrocytic stages [PMID:29649445]. Beyond this nucleolar localization and pull-down association, no enzymatic activity, structure, direct binding partner, or functional mechanism has been established for NOP5 itself in the available corpus.","teleology":[{"year":2012,"claim":"Establishing where NOP5 resides, mass spectrometry of isolated nuclei placed it in the P. falciparum nuclear proteome and flagged its prior nucleolar localization, giving a first subcellular anchor for an otherwise uncharacterized protein.","evidence":"Organellar proteomics by high-accuracy mass spectrometry of isolated parasite nuclei","pmids":["23181666"],"confidence":"Low","gaps":["Detection in a pan-nuclear catalog only; no functional experiment performed on NOP5 itself","No enzymatic activity or molecular role assigned","Nucleolar assignment cited from prior work rather than demonstrated in this study"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2018,"claim":"Asking what NOP5 associates with, DNA pull-downs showed it co-enriches with AP2-I and chromatin factors on a specific regulatory motif, providing the first (associative) link between this nucleolar protein and a transcriptional regulatory complex.","evidence":"DNA oligonucleotide pull-down with regulatory motif 028 probe followed by mass spectrometry, intraerythrocytic stages","pmids":["29649445"],"confidence":"Low","gaps":["Single large-scale pull-down without functional follow-up specific to NOP5","Association may be indirect; no reciprocal or direct binding validation for NOP5","No demonstration that NOP5 contributes to regulatory activity of the motif complex"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":null,"claim":"The direct molecular activity of NOP5, its role in nucleolar biology, and whether its association with the AP2-I regulatory motif complex is functional or incidental remain unknown.","evidence":"No direct functional, structural, or mechanistic study of NOP5 present in the corpus","pmids":[],"confidence":"Low","gaps":["No enzymatic activity or biochemical function established","No structure or direct binding partner defined","No genetic perturbation or phenotype characterized"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["Regulatory motif 028 DNA-associated complex (with AP2-I, bromodomain proteins, HMGB3, SWIB/MDM2 domain protein) [#1]"],"partners":["AP2-I (CO-ENRICHED IN MOTIF 028 DNA PULL-DOWN) [#1]","BROMODOMAIN PROTEINS (CO-ENRICHED) [#1]","HMGB3 (CO-ENRICHED) [#1]","SWIB/MDM2 DOMAIN PROTEIN (CO-ENRICHED) [#1]"],"other_free_text":["Detected in the P. falciparum nuclear proteome by mass spectrometry; cited as one of three proteins previously localized to the parasite nucleolus [#0]","Association with the regulatory DNA motif complex is from a single pull-down experiment with no NOP5-specific functional validation [#1]"]}},"prefetch_data":{},"corpus_meta":[{"pmid":"20078859","id":"PMC_20078859","title":"Assessing functional annotation transfers with inter-species conserved coexpression: application to Plasmodium falciparum.","date":"2010","source":"BMC genomics","url":"https://pubmed.ncbi.nlm.nih.gov/20078859","citation_count":13,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["curated_ref"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"23181666","id":"","title":"Organellar proteomics reveals hundreds of novel nuclear proteins in the malaria parasite Plasmodium falciparum.","date":"2012","source":"Genome biology","url":"https://pubmed.ncbi.nlm.nih.gov/23181666","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["NOP5"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"29649445","id":"","title":"Chromatin Accessibility-Based Characterization of the Gene Regulatory Network Underlying Plasmodium falciparum Blood-Stage Development.","date":"2018","source":"Cell host & microbe","url":"https://pubmed.ncbi.nlm.nih.gov/29649445","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["NOP5"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":5623,"output_tokens":1078,"usd":0.016519,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5197,"output_tokens":1652,"usd":0.033642,"stage2_stop_reason":"end_turn"},"total_usd":0.050161,"stage1_batch_id":"msgbatch_01NE1MTa8x1hW7Lo4tAaNzY1","stage2_batch_id":"msgbatch_0141vaQdeFvbo2q39AinvXM9","note":"batch pricing = 50% of standard"},"stage1_raw":"I need to carefully analyze these papers for mechanistic findings about PF3D7_1008800 (NOP5).\n\n**Paper [1] (PMID:20078859):** Computational coexpression analysis — no direct experiment on NOP5/PF3D7_1008800. This is annotation transfer by bioinformatics. EXCLUDE (Tier 4, computational only).\n\n**Paper [2] (PMID:23181666):** Nuclear proteomics study. The body mentions note that PfNOP5 (PF10_0085) was previously localized to the nucleolus — but PF10_0085 is the old locus ID. I need to check: PF3D7_1008800 corresponds to PF10_0085 (chromosome 10, gene 85). Yes, PF10_0085 = PF3D7_1008800. The paper detects NOP5 in the nuclear proteome via mass spectrometry, and references prior nucleolar localization. The proteomics detection is a pan-proteome catalog result (not mechanistic for NOP5 specifically). The nucleolar localization of NOP5 is referenced as established by prior work [refs 83,84], not by this paper directly. So this paper itself doesn't establish a new mechanistic finding about NOP5 beyond detecting it in the nuclear proteome.\n\n**Paper [3] (PMID:29649445):** DNA pull-down / ATAC-seq study. The body mentions that NOP5 was enriched in pull-downs with a de novo DNA motif (028) together with AP2-I and chromatin factors. This is a single Co-IP/pulldown result showing NOP5 associates with a DNA probe containing a specific regulatory motif. This is a Tier 3 finding — single pulldown, weak evidence.\n\nThe prior nucleolar localization of NOP5 (PF10_0085) is cited in paper [2] as already established (refs 83,84), but those papers are not in this corpus. I cannot extract from papers not in the corpus.\n\n```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2012,\n      \"finding\": \"NOP5 (PF3D7_1008800/PF10_0085) was detected in the nuclear proteome of P. falciparum by high-accuracy mass spectrometry, and is noted as one of only three proteins previously localized to the parasite nucleolus.\",\n      \"method\": \"Organellar proteomics (high-accuracy mass spectrometry of isolated nuclei)\",\n      \"journal\": \"Genome biology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — mass spectrometry detection in a pan-nuclear proteome catalog; no functional experiment performed on NOP5 itself in this paper\",\n      \"pmids\": [\"23181666\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"NOP5 (PF3D7_1008800) was enriched in DNA pull-downs using oligonucleotide probes containing de novo regulatory motif 028, together with the transcription factor AP2-I and chromatin-related factors (bromodomain proteins, HMGB3, SWIB/MDM2 domain protein), suggesting NOP5 associates with this regulatory DNA motif complex in P. falciparum intraerythrocytic stages.\",\n      \"method\": \"DNA oligonucleotide pull-down followed by mass spectrometry\",\n      \"journal\": \"Cell host & microbe\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single pull-down experiment in a large-scale study; no functional follow-up specific to NOP5\",\n      \"pmids\": [\"29649445\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"current_model\": \"NOP5 (PF3D7_1008800) is a nucleolar protein in P. falciparum detected in the nuclear proteome by mass spectrometry, and has been found associated with a regulatory DNA motif complex containing the transcription factor AP2-I and chromatin factors in pull-down experiments; no direct enzymatic activity, structure, or functional mechanism has been established for this protein.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"NOP5 (PF3D7_1008800) is a putative nucleolar protein of Plasmodium falciparum whose function has not been directly characterized in the available corpus. It was detected in the parasite nuclear proteome by high-accuracy mass spectrometry and is noted as one of only three proteins previously localized to the parasite nucleolus [#0]. In DNA oligonucleotide pull-downs using probes bearing the de novo regulatory motif 028, NOP5 co-enriched with the transcription factor AP2-I and chromatin-associated factors (bromodomain proteins, HMGB3, and a SWIB/MDM2 domain protein), placing it in physical association with a regulatory DNA motif complex during intraerythrocytic stages [#1]. Beyond this nucleolar localization and pull-down association, no enzymatic activity, structure, direct binding partner, or functional mechanism has been established for NOP5 itself in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2012,\n      \"claim\": \"Establishing where NOP5 resides, mass spectrometry of isolated nuclei placed it in the P. falciparum nuclear proteome and flagged its prior nucleolar localization, giving a first subcellular anchor for an otherwise uncharacterized protein.\",\n      \"evidence\": \"Organellar proteomics by high-accuracy mass spectrometry of isolated parasite nuclei\",\n      \"pmids\": [\"23181666\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"Detection in a pan-nuclear catalog only; no functional experiment performed on NOP5 itself\",\n        \"No enzymatic activity or molecular role assigned\",\n        \"Nucleolar assignment cited from prior work rather than demonstrated in this study\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Asking what NOP5 associates with, DNA pull-downs showed it co-enriches with AP2-I and chromatin factors on a specific regulatory motif, providing the first (associative) link between this nucleolar protein and a transcriptional regulatory complex.\",\n      \"evidence\": \"DNA oligonucleotide pull-down with regulatory motif 028 probe followed by mass spectrometry, intraerythrocytic stages\",\n      \"pmids\": [\"29649445\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"Single large-scale pull-down without functional follow-up specific to NOP5\",\n        \"Association may be indirect; no reciprocal or direct binding validation for NOP5\",\n        \"No demonstration that NOP5 contributes to regulatory activity of the motif complex\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The direct molecular activity of NOP5, its role in nucleolar biology, and whether its association with the AP2-I regulatory motif complex is functional or incidental remain unknown.\",\n      \"evidence\": \"No direct functional, structural, or mechanistic study of NOP5 present in the corpus\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No enzymatic activity or biochemical function established\",\n        \"No structure or direct binding partner defined\",\n        \"No genetic perturbation or phenotype characterized\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [],\n    \"localization\": [\n      {\"term_id\": \"GO:0005730\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"pathway\": [],\n    \"complexes\": [\n      \"Regulatory motif 028 DNA-associated complex (with AP2-I, bromodomain proteins, HMGB3, SWIB/MDM2 domain protein) [#1]\"\n    ],\n    \"partners\": [\n      \"AP2-I (co-enriched in motif 028 DNA pull-down) [#1]\",\n      \"Bromodomain proteins (co-enriched) [#1]\",\n      \"HMGB3 (co-enriched) [#1]\",\n      \"SWIB/MDM2 domain protein (co-enriched) [#1]\"\n    ],\n    \"other_free_text\": [\n      \"Detected in the P. falciparum nuclear proteome by mass spectrometry; cited as one of three proteins previously localized to the parasite nucleolus [#0]\",\n      \"Association with the regulatory DNA motif complex is from a single pull-down experiment with no NOP5-specific functional validation [#1]\"\n    ]\n  }\n}","audit_flag":null,"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_1008800","name":null,"product":"nucleolar protein 5, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_1207000","name":null,"product":"nucleolar protein 5, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_0808200","name":null,"product":"nucleolar protein 5, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"NOP5","evaluation":null}