{"gene":"PF3D7_1362100","run_date":"2026-09-08T14:19:06","timeline":{"discoveries":[{"year":2013,"finding":"PF3D7_1362100 (14-3-3II; referred to in the abstract as Pf14-3-3I) binds recombinant purified parasite histones, and using H3-specific phosphopeptides was shown to preferentially bind H3S28ph over H3S10ph, functioning as a histone H3 phosphorylation reader; in silico structural analysis confirmed that residues responsible for binding H3S10ph and/or H3S28ph are conserved at primary and tertiary structure levels.","method":"Recombinant protein pulldown with purified parasite histones; phosphopeptide binding assays with a battery of H3-specific phosphopeptides; in silico structural analysis","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct biochemical binding assays (recombinant protein + phosphopeptide panel) in single lab, supported by structural conservation analysis; multiple orthogonal methods but not independently replicated","pmids":["23308157"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2010,"finding":"PF3D7_1362100 (14-3-3II; referred to in the abstract as Plasmodium 14-3-3) associates with dematin, an actin-binding protein of the erythrocyte membrane skeleton that is internalized by the malaria parasite; in vitro, this interaction is strictly dependent on phosphorylation of dematin at Ser124 and Ser333, which belong to two 14-3-3 putative binding motifs.","method":"Co-immunoprecipitation/association assay; in vitro binding assay with phosphorylated vs. non-phosphorylated dematin","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — phosphorylation-dependent interaction demonstrated in vitro with defined serine residues, single lab, two complementary methods","pmids":["21084299"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2016,"finding":"PF3D7_1362100 (14-3-3II; referred to in the abstract as Pf14-3-3I) physically binds and colocalizes with PfAKAL (an AKAP-like protein); PF3D7_1362100 in turn interacts with the P. falciparum PKA regulatory subunit (PfPKA-R), suggesting it can bridge PfAKAL to PfPKA-R. PF3D7_1362100 is phosphorylated in vitro by PKA, indicating its interactions may be regulated by PKA-mediated phosphorylation.","method":"Pull-down experiments with recombinant proteins and parasite extracts; immunofluorescence colocalization; radiolabel kinase activity assay (in vitro phosphorylation by PKA); proteomic/biochemical approaches","journal":"Malaria journal","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal pulldown and colocalization plus in vitro kinase assay in single lab, multiple orthogonal methods","pmids":["27129434"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":"3D7"}]}],"current_model":"PF3D7_1362100 (14-3-3II) is a multifunctional phospho-reader/scaffold protein in P. falciparum that (1) binds histone H3 phosphorylated at S28 (preferentially over H3S10ph) in the nucleus, (2) associates with internalized erythrocyte dematin in a phosphorylation-dependent manner (requiring dematin Ser124 and Ser333), and (3) bridges the AKAP-like protein PfAKAL to the PKA regulatory subunit PfPKA-R, with PF3D7_1362100 itself being phosphorylated by PKA in vitro."},"narrative":{"mechanistic_narrative":"PF3D7_1362100 (14-3-3II) is a phosphorylation-dependent reader and scaffold protein in Plasmodium falciparum that couples phospho-signaling to distinct cellular compartments [PMID:23308157, PMID:21084299, PMID:27129434]. In the context of chromatin, it binds parasite histone H3 and acts as a phospho-reader with preference for H3S28ph over H3S10ph, a selectivity consistent with conservation of the phosphopeptide-binding residues [PMID:23308157]. It also engages the erythrocyte membrane-skeleton protein dematin after the latter is internalized by the parasite, an interaction that strictly requires dematin phosphorylation at Ser124 and Ser333, two canonical 14-3-3 binding motifs [PMID:21084299]. In a PKA-signaling context, PF3D7_1362100 physically binds and colocalizes with the AKAP-like protein PfAKAL and additionally interacts with the PKA regulatory subunit PfPKA-R, positioning it to bridge PfAKAL to PfPKA-R; it is itself phosphorylated in vitro by PKA, indicating its scaffold interactions are subject to PKA-mediated regulation [PMID:27129434]. Beyond these three phosphorylation-dependent binding activities, no further mechanistic detail—including in vivo functional consequences or a knockout phenotype—has been characterized in the available corpus.","teleology":[{"year":2010,"claim":"Established that PF3D7_1362100 can capture a host-derived substrate in a phospho-specific manner, defining it as a phosphorylation-dependent binding module rather than a constitutive interactor.","evidence":"Co-immunoprecipitation and in vitro binding of phosphorylated versus non-phosphorylated erythrocyte dematin","pmids":["21084299"],"confidence":"Medium","gaps":["Functional consequence of the dematin interaction for the parasite is unknown","The kinase phosphorylating dematin Ser124/Ser333 in this context is not identified","Interaction shown in vitro; not validated in situ within the parasite"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2013,"claim":"Answered whether PF3D7_1362100 reads chromatin marks by showing it selectively binds phospho-histone H3, establishing a nuclear phospho-reader activity with defined mark preference.","evidence":"Recombinant pulldown with parasite histones plus an H3 phosphopeptide panel, supported by in silico structural conservation analysis","pmids":["23308157"],"confidence":"Medium","gaps":["Downstream chromatin/transcriptional consequence of H3S28ph reading not defined","In vivo occupancy on parasite chromatin not demonstrated","The kinase generating H3S28ph is not identified"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2016,"claim":"Placed PF3D7_1362100 in the PKA signaling architecture by showing it bridges an AKAP-like protein to the PKA regulatory subunit and is itself a PKA substrate, implicating it as a scaffold whose interactions are regulated by phosphorylation.","evidence":"Reciprocal pulldowns with recombinant proteins and parasite extracts, immunofluorescence colocalization, and an in vitro radiolabel PKA kinase assay","pmids":["27129434"],"confidence":"Medium","gaps":["The functional output of the PfAKAL–PF3D7_1362100–PfPKA-R bridge is not demonstrated in vivo","The residue(s) on PF3D7_1362100 phosphorylated by PKA are not mapped","Whether PKA phosphorylation enhances or disrupts specific interactions is untested"],"attribution":[{"species":"Plasmodium falciparum","strain":"3D7"}]},{"year":null,"claim":"Whether the three characterized activities—H3S28ph reading, dematin binding, and PKA-scaffolding—operate independently or as part of a unified regulatory program, and the in vivo phenotype of PF3D7_1362100 loss, remain unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No genetic knockout or knockdown phenotype in the corpus","No structural model of PF3D7_1362100 bound to any of its partners","Temporal/stage regulation of the three binding activities not addressed"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["PfAKAL–PF3D7_1362100–PfPKA-R bridging assembly"],"partners":["PARASITE HISTONE H3 (H3S28PH)","ERYTHROCYTE DEMATIN (PHOSPHO-SER124/SER333)","PFAKAL (AKAP-LIKE PROTEIN)","PFPKA-R (PKA REGULATORY SUBUNIT)"],"other_free_text":["Acts as a phosphorylation-dependent reader/scaffold; binding to dematin requires phospho-Ser124 and phospho-Ser333, and binding to H3 favors S28ph over S10ph [#0, #1]","Is itself a substrate for phosphorylation by PKA in vitro, implying auto-regulation of its scaffold interactions [#2]","Abstracts refer to this gene as 'Pf14-3-3I' and 'Plasmodium 14-3-3'; these labels denote PF3D7_1362100 (14-3-3II) in this corpus"]}},"prefetch_data":{},"corpus_meta":[{"pmid":"23308157","id":"PMC_23308157","title":"Comprehensive histone phosphorylation analysis and identification of Pf14-3-3 protein as a histone H3 phosphorylation reader in malaria parasites.","date":"2013","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/23308157","citation_count":31,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["curated_ref"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"21084299","id":"PMC_21084299","title":"Dematin, a component of the erythrocyte membrane skeleton, is internalized by the malaria parasite and associates with Plasmodium 14-3-3.","date":"2010","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/21084299","citation_count":27,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["curated_ref"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"22984113","id":"PMC_22984113","title":"High levels of immunoglobulin E autoantibody to 14-3-3 epsilon protein correlate with protection against severe Plasmodium falciparum malaria.","date":"2012","source":"The Journal of infectious diseases","url":"https://pubmed.ncbi.nlm.nih.gov/22984113","citation_count":15,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["14-3-3 protein"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"27129434","id":"PMC_27129434","title":"Characterization of an A-kinase anchoring protein-like suggests an alternative way of PKA anchoring in Plasmodium falciparum.","date":"2016","source":"Malaria journal","url":"https://pubmed.ncbi.nlm.nih.gov/27129434","citation_count":6,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["14-3-3 protein"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":10320,"output_tokens":1814,"usd":0.045365,"retried_sync":true},"stage2":{"model":"claude-opus-4-8","input_tokens":5900,"output_tokens":2322,"usd":0.043775,"stage2_stop_reason":"end_turn"},"total_usd":0.08914,"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\": 2013,\n      \"finding\": \"PF3D7_1362100 (14-3-3II; referred to in the abstract as Pf14-3-3I) binds recombinant purified parasite histones, and using H3-specific phosphopeptides was shown to preferentially bind H3S28ph over H3S10ph, functioning as a histone H3 phosphorylation reader; in silico structural analysis confirmed that residues responsible for binding H3S10ph and/or H3S28ph are conserved at primary and tertiary structure levels.\",\n      \"method\": \"Recombinant protein pulldown with purified parasite histones; phosphopeptide binding assays with a battery of H3-specific phosphopeptides; in silico structural analysis\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct biochemical binding assays (recombinant protein + phosphopeptide panel) in single lab, supported by structural conservation analysis; multiple orthogonal methods but not independently replicated\",\n      \"pmids\": [\"23308157\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"PF3D7_1362100 (14-3-3II; referred to in the abstract as Plasmodium 14-3-3) associates with dematin, an actin-binding protein of the erythrocyte membrane skeleton that is internalized by the malaria parasite; in vitro, this interaction is strictly dependent on phosphorylation of dematin at Ser124 and Ser333, which belong to two 14-3-3 putative binding motifs.\",\n      \"method\": \"Co-immunoprecipitation/association assay; in vitro binding assay with phosphorylated vs. non-phosphorylated dematin\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — phosphorylation-dependent interaction demonstrated in vitro with defined serine residues, single lab, two complementary methods\",\n      \"pmids\": [\"21084299\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"PF3D7_1362100 (14-3-3II; referred to in the abstract as Pf14-3-3I) physically binds and colocalizes with PfAKAL (an AKAP-like protein); PF3D7_1362100 in turn interacts with the P. falciparum PKA regulatory subunit (PfPKA-R), suggesting it can bridge PfAKAL to PfPKA-R. PF3D7_1362100 is phosphorylated in vitro by PKA, indicating its interactions may be regulated by PKA-mediated phosphorylation.\",\n      \"method\": \"Pull-down experiments with recombinant proteins and parasite extracts; immunofluorescence colocalization; radiolabel kinase activity assay (in vitro phosphorylation by PKA); proteomic/biochemical approaches\",\n      \"journal\": \"Malaria journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal pulldown and colocalization plus in vitro kinase assay in single lab, multiple orthogonal methods\",\n      \"pmids\": [\"27129434\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"3D7\"}\n      ]\n    }\n  ],\n  \"current_model\": \"PF3D7_1362100 (14-3-3II) is a multifunctional phospho-reader/scaffold protein in P. falciparum that (1) binds histone H3 phosphorylated at S28 (preferentially over H3S10ph) in the nucleus, (2) associates with internalized erythrocyte dematin in a phosphorylation-dependent manner (requiring dematin Ser124 and Ser333), and (3) bridges the AKAP-like protein PfAKAL to the PKA regulatory subunit PfPKA-R, with PF3D7_1362100 itself being phosphorylated by PKA in vitro.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PF3D7_1362100 (14-3-3II) is a phosphorylation-dependent reader and scaffold protein in Plasmodium falciparum that couples phospho-signaling to distinct cellular compartments [#0, #1, #2]. In the context of chromatin, it binds parasite histone H3 and acts as a phospho-reader with preference for H3S28ph over H3S10ph, a selectivity consistent with conservation of the phosphopeptide-binding residues [#0]. It also engages the erythrocyte membrane-skeleton protein dematin after the latter is internalized by the parasite, an interaction that strictly requires dematin phosphorylation at Ser124 and Ser333, two canonical 14-3-3 binding motifs [#1]. In a PKA-signaling context, PF3D7_1362100 physically binds and colocalizes with the AKAP-like protein PfAKAL and additionally interacts with the PKA regulatory subunit PfPKA-R, positioning it to bridge PfAKAL to PfPKA-R; it is itself phosphorylated in vitro by PKA, indicating its scaffold interactions are subject to PKA-mediated regulation [#2]. Beyond these three phosphorylation-dependent binding activities, no further mechanistic detail—including in vivo functional consequences or a knockout phenotype—has been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2010,\n      \"claim\": \"Established that PF3D7_1362100 can capture a host-derived substrate in a phospho-specific manner, defining it as a phosphorylation-dependent binding module rather than a constitutive interactor.\",\n      \"evidence\": \"Co-immunoprecipitation and in vitro binding of phosphorylated versus non-phosphorylated erythrocyte dematin\",\n      \"pmids\": [\"21084299\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Functional consequence of the dematin interaction for the parasite is unknown\",\n        \"The kinase phosphorylating dematin Ser124/Ser333 in this context is not identified\",\n        \"Interaction shown in vitro; not validated in situ within the parasite\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Answered whether PF3D7_1362100 reads chromatin marks by showing it selectively binds phospho-histone H3, establishing a nuclear phospho-reader activity with defined mark preference.\",\n      \"evidence\": \"Recombinant pulldown with parasite histones plus an H3 phosphopeptide panel, supported by in silico structural conservation analysis\",\n      \"pmids\": [\"23308157\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Downstream chromatin/transcriptional consequence of H3S28ph reading not defined\",\n        \"In vivo occupancy on parasite chromatin not demonstrated\",\n        \"The kinase generating H3S28ph is not identified\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Placed PF3D7_1362100 in the PKA signaling architecture by showing it bridges an AKAP-like protein to the PKA regulatory subunit and is itself a PKA substrate, implicating it as a scaffold whose interactions are regulated by phosphorylation.\",\n      \"evidence\": \"Reciprocal pulldowns with recombinant proteins and parasite extracts, immunofluorescence colocalization, and an in vitro radiolabel PKA kinase assay\",\n      \"pmids\": [\"27129434\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"The functional output of the PfAKAL–PF3D7_1362100–PfPKA-R bridge is not demonstrated in vivo\",\n        \"The residue(s) on PF3D7_1362100 phosphorylated by PKA are not mapped\",\n        \"Whether PKA phosphorylation enhances or disrupts specific interactions is untested\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"3D7\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Whether the three characterized activities—H3S28ph reading, dematin binding, and PKA-scaffolding—operate independently or as part of a unified regulatory program, and the in vivo phenotype of PF3D7_1362100 loss, remain unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No genetic knockout or knockdown phenotype in the corpus\",\n        \"No structural model of PF3D7_1362100 bound to any of its partners\",\n        \"Temporal/stage regulation of the three binding activities not addressed\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0042826\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0050815\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"GO:0030674\", \"supporting_discovery_ids\": [2]},\n      {\"term_id\": \"GO:0019904\", \"supporting_discovery_ids\": [1, 2]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0034605\", \"supporting_discovery_ids\": [2]}\n    ],\n    \"complexes\": [\n      \"PfAKAL–PF3D7_1362100–PfPKA-R bridging assembly\"\n    ],\n    \"partners\": [\n      \"parasite histone H3 (H3S28ph)\",\n      \"erythrocyte dematin (phospho-Ser124/Ser333)\",\n      \"PfAKAL (AKAP-like protein)\",\n      \"PfPKA-R (PKA regulatory subunit)\"\n    ],\n    \"other_free_text\": [\n      \"Acts as a phosphorylation-dependent reader/scaffold; binding to dematin requires phospho-Ser124 and phospho-Ser333, and binding to H3 favors S28ph over S10ph [#0, #1]\",\n      \"Is itself a substrate for phosphorylation by PKA in vitro, implying auto-regulation of its scaffold interactions [#2]\",\n      \"Abstracts refer to this gene as 'Pf14-3-3I' and 'Plasmodium 14-3-3'; these labels denote PF3D7_1362100 (14-3-3II) in this corpus\"\n    ]\n  }\n}","audit_flag":{"gene":"PF3D7_1362100","tier":"IDENTITY_CHECK","verdict":"identity unverified","subtype":"names_other_cards","uniprot_band":"","rules_fired":"R12","issue":"No cited paper names this card; 2 of 3 cited papers name other catalogue genes (PF3D7_0818200, PF3D7_0512900, PF3D7_0934800). The summary may describe one of those genes."},"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_1362100","name":null,"product":"14-3-3 protein","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_1138100","name":null,"product":"14-3-3 protein, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_1109200","name":null,"product":"14-3-3 protein, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"","evaluation":null}