{"gene":"PF3D7_1002100","run_date":"2026-09-08T12:51:27","timeline":{"discoveries":[{"year":2008,"finding":"PTP5 (PF3D7_1002100) was identified as one of eight exported proteins required for trafficking of PfEMP1 to the infected erythrocyte surface and for assembly of knobs; knockout of PTP5 abolished PfEMP1 export and knob formation, establishing its role as a component of the parasite's host-cell remodeling machinery.","method":"Large-scale gene knockout combined with functional screens (PfEMP1 export assay, knob assembly assay) in P. falciparum","journal":"Cell","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — clean KO with defined cellular phenotype (loss of PfEMP1 export and knobs), single lab, large-scale screen context with functional readouts for multiple genes including PTP5","pmids":["18614010"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2018,"finding":"PTP5 directly interacts with PfPV1 (a merozoite dense granule protein localized to the parasitophorous vacuole): co-immunoprecipitation with anti-PfPV1 antibody pulled down PTP5, and surface plasmon resonance confirmed direct protein-protein interaction. A C-terminal region of PTP5 designated the PfPV1 High-affinity Region (PHR) was identified as the dominant binding site. A PTP5 mutant lacking PHR (PTP5ΔPHR) showed arrested export to the infected erythrocyte cytosol, indicating PHR is essential for PTP5 export.","method":"Co-immunoprecipitation, surface plasmon resonance (SPR), structured illumination microscopy (SIM) of export-arrested mutant, deletion mutagenesis","journal":"Scientific reports","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — multiple orthogonal methods (Co-IP, SPR, deletion mutagenesis, SIM) in a single focused study directly characterizing PTP5","pmids":["29487358"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"current_model":"PTP5 (PF3D7_1002100) is an exported P. falciparum protein required for trafficking of PfEMP1 to the infected erythrocyte surface and knob assembly; it is directly bound by the parasitophorous vacuole dense granule protein PfPV1 via a C-terminal high-affinity region (PHR) on PTP5, and this interaction is necessary for PTP5's own export into the host erythrocyte cytosol."},"narrative":{"mechanistic_narrative":"PTP5 (PF3D7_1002100) is an exported Plasmodium falciparum protein that functions in host erythrocyte remodeling, specifically in the trafficking of the virulence adhesin PfEMP1 to the infected red-cell surface and in knob assembly; knockout of PTP5 abolishes both PfEMP1 export and knob formation, placing it among the parasite's essential host-cell remodeling machinery [PMID:18614010]. PTP5 export from the parasite into the host erythrocyte cytosol depends on a direct interaction with the parasitophorous vacuole dense granule protein PfPV1, mediated by a C-terminal PfPV1 High-affinity Region (PHR) on PTP5; deletion of the PHR arrests PTP5 export, establishing this interaction as necessary for PTP5's own delivery into the host cell [PMID:29487358]. Beyond its role in PfEMP1 trafficking, knob assembly, and its PfPV1-dependent export, no further mechanistic detail for PTP5 has been characterized in the available corpus.","teleology":[{"year":2008,"claim":"Establishing whether PTP5 is functionally required for the parasite's export of its major virulence adhesin, this work showed PTP5 is one of the exported factors whose loss abolishes PfEMP1 surface trafficking and knob formation.","evidence":"Large-scale gene knockout with PfEMP1 export and knob assembly functional readouts in P. falciparum","pmids":["18614010"],"confidence":"Medium","gaps":["Does not define the molecular step at which PTP5 acts in the trafficking pathway","No direct binding partners or biochemical activity identified","Whether PTP5 acts on PfEMP1 directly or indirectly is unresolved"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2018,"claim":"Addressing how PTP5 itself reaches the host cytosol, this work identified a direct PTP5–PfPV1 interaction via a C-terminal PHR and showed the PHR is required for PTP5 export, linking parasitophorous vacuole PfPV1 to PTP5 trafficking.","evidence":"Co-immunoprecipitation, surface plasmon resonance, deletion mutagenesis, and structured illumination microscopy of an export-arrested PTP5ΔPHR mutant in P. falciparum","pmids":["29487358"],"confidence":"High","gaps":["Structural basis of the PHR–PfPV1 interaction is not resolved","Whether PfPV1 binding to PTP5 is required downstream for PfEMP1 trafficking specifically is not shown","Mechanism connecting PTP5 export to knob assembly remains undefined"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":null,"claim":"The molecular activity of PTP5 within the PfEMP1 trafficking pathway — including any direct cargo binding, its interactors in the host cytosol, and how it contributes to knob assembly — remains unknown.","evidence":"No further mechanistic characterization of PTP5 in the available corpus","pmids":[],"confidence":"Medium","gaps":["No direct PTP5–PfEMP1 interaction demonstrated","No structural model of PTP5","No definition of PTP5's biochemical role in knob assembly"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":[],"partners":["PFPV1 (PARASITOPHOROUS VACUOLE DENSE GRANULE PROTEIN; DIRECT BINDING VIA PTP5 C-TERMINAL PHR) [#1]","PFEMP1 (FUNCTIONALLY REQUIRED FOR ITS EXPORT; DIRECT INTERACTION NOT ESTABLISHED) [#0]"],"other_free_text":["PTP5 is one of eight exported proteins required for PfEMP1 trafficking and knob formation; knockout abolishes both [#0].","A C-terminal PfPV1 High-affinity Region (PHR) on PTP5 is essential for PTP5 export into the host erythrocyte cytosol [#1]."]}},"prefetch_data":{},"corpus_meta":[{"pmid":"18614010","id":"PMC_18614010","title":"Exported proteins required for virulence and rigidity of Plasmodium falciparum-infected human erythrocytes.","date":"2008","source":"Cell","url":"https://pubmed.ncbi.nlm.nih.gov/18614010","citation_count":410,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["curated_ref"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"18785843","id":"PMC_18785843","title":"Antigenic variation in Plasmodium falciparum.","date":"2008","source":"Annual review of microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/18785843","citation_count":338,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["PfEMP1"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"11071284","id":"PMC_11071284","title":"Classification of adhesive domains in the Plasmodium falciparum erythrocyte membrane protein 1 family.","date":"2000","source":"Molecular and biochemical parasitology","url":"https://pubmed.ncbi.nlm.nih.gov/11071284","citation_count":224,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["PfEMP1"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"22619319","id":"PMC_22619319","title":"Plasmodium falciparum erythrocyte membrane protein 1 domain cassettes 8 and 13 are associated with severe malaria in children.","date":"2012","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/22619319","citation_count":222,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["PfEMP1"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"16814594","id":"PMC_16814594","title":"A family affair: var genes, PfEMP1 binding, and malaria disease.","date":"2006","source":"Current opinion in microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/16814594","citation_count":221,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["PfEMP1"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"19402747","id":"PMC_19402747","title":"Sir2 paralogues cooperate to regulate virulence genes and antigenic variation in Plasmodium falciparum.","date":"2009","source":"PLoS biology","url":"https://pubmed.ncbi.nlm.nih.gov/19402747","citation_count":199,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["PfEMP1"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"23957661","id":"PMC_23957661","title":"Malaria's deadly grip: cytoadhesion of Plasmodium falciparum-infected erythrocytes.","date":"2013","source":"Cellular microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/23957661","citation_count":179,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["PfEMP1"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"28603279","id":"PMC_28603279","title":"Variant surface antigens of Plasmodium falciparum and their roles in severe malaria.","date":"2017","source":"Nature reviews. 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infection","url":"https://pubmed.ncbi.nlm.nih.gov/39182654","citation_count":8,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["PfEMP1"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":47183,"output_tokens":1053,"usd":0.078672,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5395,"output_tokens":1794,"usd":0.035912,"stage2_stop_reason":"end_turn"},"total_usd":0.114584,"stage1_batch_id":"msgbatch_01DisAaTypwmC8QwdMBuePHo","stage2_batch_id":"msgbatch_0184zxZTqxiEfdYYfPMfkqjb","note":"batch pricing = 50% of standard"},"stage1_raw":"Looking through the corpus, I need to find papers specifically about PF3D7_1002100 (PTP5), not about PfEMP1 or other genes. The vast majority of these papers are about PfEMP1, var genes, and related biology — not about PTP5 specifically.\n\nPaper [73] (PMID: 29487358) is the key one: it explicitly mentions \"exported protein PTP5\" and characterizes its interaction with PfPV1. Paper [1] (PMID: 18614010) identifies proteins required for PfEMP1 export including genes from a knockout screen — PTP5 is one of the \"PfEMP1-trafficking proteins\" identified. Paper [77] (PMID: 40929367) mentions \"exported parasite genes involved in the trafficking of the P. falciparum erythrocyte membrane protein 1 (PfEMP1) ligand\" but doesn't specifically name PTP5. Paper [86] (PMID: 41460168) surveys \"protein environment from functional PfEMP1 in the host cell\" and identifies \"new proteins needed for PfEMP1-mediated sequestration\" but doesn't specifically name PTP5.\n\nOnly papers [1] and [73] specifically mention PTP5 (PF3D7_1002100).\n\n```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2008,\n      \"finding\": \"PTP5 (PF3D7_1002100) was identified as one of eight exported proteins required for trafficking of PfEMP1 to the infected erythrocyte surface and for assembly of knobs; knockout of PTP5 abolished PfEMP1 export and knob formation, establishing its role as a component of the parasite's host-cell remodeling machinery.\",\n      \"method\": \"Large-scale gene knockout combined with functional screens (PfEMP1 export assay, knob assembly assay) in P. falciparum\",\n      \"journal\": \"Cell\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean KO with defined cellular phenotype (loss of PfEMP1 export and knobs), single lab, large-scale screen context with functional readouts for multiple genes including PTP5\",\n      \"pmids\": [\"18614010\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"PTP5 directly interacts with PfPV1 (a merozoite dense granule protein localized to the parasitophorous vacuole): co-immunoprecipitation with anti-PfPV1 antibody pulled down PTP5, and surface plasmon resonance confirmed direct protein-protein interaction. A C-terminal region of PTP5 designated the PfPV1 High-affinity Region (PHR) was identified as the dominant binding site. A PTP5 mutant lacking PHR (PTP5ΔPHR) showed arrested export to the infected erythrocyte cytosol, indicating PHR is essential for PTP5 export.\",\n      \"method\": \"Co-immunoprecipitation, surface plasmon resonance (SPR), structured illumination microscopy (SIM) of export-arrested mutant, deletion mutagenesis\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — multiple orthogonal methods (Co-IP, SPR, deletion mutagenesis, SIM) in a single focused study directly characterizing PTP5\",\n      \"pmids\": [\"29487358\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"current_model\": \"PTP5 (PF3D7_1002100) is an exported P. falciparum protein required for trafficking of PfEMP1 to the infected erythrocyte surface and knob assembly; it is directly bound by the parasitophorous vacuole dense granule protein PfPV1 via a C-terminal high-affinity region (PHR) on PTP5, and this interaction is necessary for PTP5's own export into the host erythrocyte cytosol.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PTP5 (PF3D7_1002100) is an exported Plasmodium falciparum protein that functions in host erythrocyte remodeling, specifically in the trafficking of the virulence adhesin PfEMP1 to the infected red-cell surface and in knob assembly; knockout of PTP5 abolishes both PfEMP1 export and knob formation, placing it among the parasite's essential host-cell remodeling machinery [#0]. PTP5 export from the parasite into the host erythrocyte cytosol depends on a direct interaction with the parasitophorous vacuole dense granule protein PfPV1, mediated by a C-terminal PfPV1 High-affinity Region (PHR) on PTP5; deletion of the PHR arrests PTP5 export, establishing this interaction as necessary for PTP5's own delivery into the host cell [#1]. Beyond its role in PfEMP1 trafficking, knob assembly, and its PfPV1-dependent export, no further mechanistic detail for PTP5 has been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2008,\n      \"claim\": \"Establishing whether PTP5 is functionally required for the parasite's export of its major virulence adhesin, this work showed PTP5 is one of the exported factors whose loss abolishes PfEMP1 surface trafficking and knob formation.\",\n      \"evidence\": \"Large-scale gene knockout with PfEMP1 export and knob assembly functional readouts in P. falciparum\",\n      \"pmids\": [\"18614010\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Does not define the molecular step at which PTP5 acts in the trafficking pathway\",\n        \"No direct binding partners or biochemical activity identified\",\n        \"Whether PTP5 acts on PfEMP1 directly or indirectly is unresolved\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Addressing how PTP5 itself reaches the host cytosol, this work identified a direct PTP5–PfPV1 interaction via a C-terminal PHR and showed the PHR is required for PTP5 export, linking parasitophorous vacuole PfPV1 to PTP5 trafficking.\",\n      \"evidence\": \"Co-immunoprecipitation, surface plasmon resonance, deletion mutagenesis, and structured illumination microscopy of an export-arrested PTP5ΔPHR mutant in P. falciparum\",\n      \"pmids\": [\"29487358\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Structural basis of the PHR–PfPV1 interaction is not resolved\",\n        \"Whether PfPV1 binding to PTP5 is required downstream for PfEMP1 trafficking specifically is not shown\",\n        \"Mechanism connecting PTP5 export to knob assembly remains undefined\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The molecular activity of PTP5 within the PfEMP1 trafficking pathway — including any direct cargo binding, its interactors in the host cytosol, and how it contributes to knob assembly — remains unknown.\",\n      \"evidence\": \"No further mechanistic characterization of PTP5 in the available corpus\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No direct PTP5–PfEMP1 interaction demonstrated\",\n        \"No structural model of PTP5\",\n        \"No definition of PTP5's biochemical role in knob assembly\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"protein binding\", \"supporting_discovery_ids\": [1]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"host cell cytoplasm\", \"supporting_discovery_ids\": [1]},\n      {\"term_id\": \"extracellular region (exported protein)\", \"supporting_discovery_ids\": [0, 1]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"protein transport into host cell\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"cytoadherence / knob assembly at infected erythrocyte surface\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\n      \"PfPV1 (parasitophorous vacuole dense granule protein; direct binding via PTP5 C-terminal PHR) [#1]\",\n      \"PfEMP1 (functionally required for its export; direct interaction not established) [#0]\"\n    ],\n    \"other_free_text\": [\n      \"PTP5 is one of eight exported proteins required for PfEMP1 trafficking and knob formation; knockout abolishes both [#0].\",\n      \"A C-terminal PfPV1 High-affinity Region (PHR) on PTP5 is essential for PTP5 export into the host erythrocyte cytosol [#1].\"\n    ]\n  }\n}","audit_flag":null,"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_1002100","name":null,"product":"EMP1-trafficking protein","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"PTP5","evaluation":null}