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and STEVOR variant surface antigen families.","date":"2022","source":"BMC bioinformatics","url":"https://pubmed.ncbi.nlm.nih.gov/34991452","citation_count":2,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["rifin"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"38910420","id":"PMC_38910420","title":"Variable Surface Antigens of Plasmodium falciparum: Protein Families with Divergent Roles.","date":"2024","source":"Protein and peptide letters","url":"https://pubmed.ncbi.nlm.nih.gov/38910420","citation_count":1,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["rifin"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"41314148","id":"PMC_41314148","title":"A subset of Plasmodium falciparum RIFINs is linked to severe malaria risk reduction and engages LILRB1 through a conserved structural 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receptors.","date":"2018","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/29443969","citation_count":1,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["rifin"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"38857964","id":"PMC_38857964","title":"[Bibliometric analysis of researches on the Plasmodium falciparum repetitive interspersed families of polypeptides protein from 1993 to 2022].","date":"2024","source":"Zhongguo xue xi chong bing fang zhi za zhi = Chinese journal of schistosomiasis control","url":"https://pubmed.ncbi.nlm.nih.gov/38857964","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["rifin"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"40562206","id":"PMC_40562206","title":"Method for deletion of variant surface antigen genes at subtelomeric region of Plasmodium 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diseases","url":"https://pubmed.ncbi.nlm.nih.gov/41492925","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["rifin"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"39950472","id":"PMC_39950472","title":"A Potential Regulatory Network of Selected Human Erythrocytic miRNAs with Plasmodium falciparum 3D7 mRNAs: A Computational Analysis.","date":"2025","source":"MicroRNA (Shariqah, United Arab Emirates)","url":"https://pubmed.ncbi.nlm.nih.gov/39950472","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["rifin"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"31687959","id":"PMC_31687959","title":"[SEVERE FORMS OF TROPICAL MALARIA: MOLECULAR GENETIC FEATURES OF THE COURSE OF THE INFECTION (REVIEW)].","date":"2019","source":"Georgian medical news","url":"https://pubmed.ncbi.nlm.nih.gov/31687959","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["rifin"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":43494,"output_tokens":5769,"usd":0.108508,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":12025,"output_tokens":5691,"usd":0.1012,"stage2_stop_reason":"end_turn"},"total_usd":0.209708,"stage1_batch_id":"msgbatch_01DbiymDmubkPpYvdbAu5a7V","stage2_batch_id":"msgbatch_012TbrWvMRH129T7PQ4SmvrJ","note":"batch pricing = 50% of standard","patch_2026_09_11":["family rifin: member shows the shared family summary only"]},"stage1_raw":"I need to carefully analyze these abstracts to extract mechanistic findings about PF3D7_0100200 specifically. However, I note that PF3D7_0100200 is described as a rifin, and the corpus is dominated by papers about the RIFIN family generally (150-200 members). Most papers discuss the RIFIN family as a whole, not PF3D7_0100200 specifically.\n\nI need to determine: which papers, if any, establish mechanistic findings about PF3D7_0100200 specifically? The corpus papers largely address the RIFIN family collectively, individual named members (like PFI0050c, PF13_0006, PF13_0006), or subgroups (A-type, B-type). None explicitly identify PF3D7_0100200 by its locus ID in a mechanistic experiment.\n\nGiven that PF3D7_0100200 is a rifin family member, I can only attribute family-level findings to it if the papers establish those findings for the whole family (i.e., all/most RIFINs). I must not adopt findings from specific named paralogs as being about PF3D7_0100200.\n\nLet me extract what applies broadly to RIFINs as a class (which PF3D7_0100200 belongs to), being careful to note these are family-level findings that include PF3D7_0100200 as a member.\n\n```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 1999,\n      \"finding\": \"RIFINs (the protein family to which PF3D7_0100200 belongs) are expressed on the surface of P. falciparum-infected red blood cells; surface localization was established by surface labeling, immunoprecipitation, and agglutination assays showing trypsin-resistant surface epitopes on parasitized RBCs.\",\n      \"method\": \"Surface radioiodination, immunoprecipitation, trypsin treatment, agglutination assays, 2D electrophoresis\",\n      \"journal\": \"The Journal of experimental medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal surface-labeling methods in a single study; finding applies to the RIFIN family broadly, not PF3D7_0100200 specifically\",\n      \"pmids\": [\"10562315\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 1999,\n      \"finding\": \"RIFINs (family including PF3D7_0100200) are clonally variant proteins encoded by the rif multigene family and localized to the surface of infected red blood cells; this was established by expression studies and surface localization consistent with a role in host-parasite interaction.\",\n      \"method\": \"Gene family characterization, expression analysis, surface localization by antibody staining\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — family-level surface localization with multiple methods but no specific functional mechanism for PF3D7_0100200\",\n      \"pmids\": [\"10430943\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"Within the RIFIN family, A-type RIFINs are transported to the surface of infected erythrocytes via Maurer's clefts, whereas B-type RIFINs are mostly retained inside the parasite; both subtypes are also expressed in merozoites, with A-type in the apical region and B-type in the cytosol. PF3D7_0100200 is a rifin family member and subject to this subfamily classification, but its specific subtype was not individually confirmed in these experiments.\",\n      \"method\": \"Indirect immunofluorescence assay, confocal microscopy, antibody staining of specific RIFIN variants\",\n      \"journal\": \"Molecular and biochemical parasitology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — subfamily localization patterns established for representative members, not for PF3D7_0100200 specifically\",\n      \"pmids\": [\"17719658\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"A specific RIFIN (PFI0050c, not PF3D7_0100200) tagged with GFP was trafficked to Maurer's clefts when internally GFP-tagged, but not to the erythrocyte surface; the C-terminal domain prevented export beyond Maurer's clefts, and truncation of C-terminal sequences allowed MC targeting. Trafficking was Brefeldin A-sensitive in young rings. The hypervariable region was exposed to the erythrocyte cytosol in MC membrane. This is a sibling RIFIN member, not PF3D7_0100200.\",\n      \"method\": \"GFP-tagging and live-cell fluorescence microscopy, selective permeabilization, Brefeldin A treatment, transfection\",\n      \"journal\": \"Traffic (Copenhagen, Denmark)\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 2 / Weak — rigorous localization experiment but on PFI0050c (a different rifin paralog), not PF3D7_0100200; included only as family context\",\n      \"pmids\": [\"17014697\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"3D7\"}]\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"RIFINs and PfEMP1 share a common trafficking pathway through the infected erythrocyte cytosol via small single vesicles (SSV), large multimeric vesicle (LMV) assemblies, and large spindle-like vesicles (LSLV) to reach the erythrocyte surface. RIFINs co-traffic with PfEMP1 and Pf332 in sub-compartmentalized LMV. LMV formation was independent of KAHRP.\",\n      \"method\": \"Immunofluorescence microscopy with RIFIN- and PfEMP1-specific antibodies, BODIPY-ceramide lipid staining, vesicle tracking\",\n      \"journal\": \"Molecular and biochemical parasitology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — family-level trafficking pathway established; not specific to PF3D7_0100200\",\n      \"pmids\": [\"14668007\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Plasmepsin V (an endoplasmic reticulum protease) cleaves the N-terminal PEXEL motif of RIFINs (and STEVORs, RESA), which is necessary for their export from the parasite. This processing is required for the export of RIFIN family members including PF3D7_0100200.\",\n      \"method\": \"In vitro Plasmepsin V cleavage assay, substrate mutagenesis, N-terminal sequencing\",\n      \"journal\": \"Traffic (Copenhagen, Denmark)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro enzymatic assay with mutagenesis of PEXEL substrates; finding applies to the RIFIN family broadly, including PF3D7_0100200 as a PEXEL-containing member\",\n      \"pmids\": [\"23387285\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"RIFINs expressed on the surface of infected RBCs bind to uninfected RBCs (preferentially blood group A) to form large rosettes and mediate microvascular binding of iRBCs. This rosette-forming adhesin activity was demonstrated by antibody blocking and blood group-specific binding assays.\",\n      \"method\": \"Rosetting assays, antibody inhibition, blood group-specific binding experiments, flow cytometry\",\n      \"journal\": \"Nature medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — functional adhesion assays with antibody blocking; family-level finding, not specific to PF3D7_0100200\",\n      \"pmids\": [\"25751816\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"A subset of RIFINs binds to the inhibitory immune receptors LILRB1 or LAIR1 on the surface of infected erythrocytes. LILRB1-binding RIFINs inhibit activation of LILRB1-expressing B cells and NK cells, demonstrating a direct immune evasion mechanism via inhibitory receptor engagement.\",\n      \"method\": \"Receptor binding assays (LILRB1, LAIR1), B cell and NK cell activation reporter assays, flow cytometry of patient-isolated infected erythrocytes\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct binding and functional immune suppression assays; family-level subset finding, not specifically PF3D7_0100200\",\n      \"pmids\": [\"29186116\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Crystal structure of a RIFIN bound to LILRB1 showed that RIFIN mimics the natural activating ligand MHC class I in its LILRB1-binding mode. A single mutation in the RIFIN disrupted the complex, blocked LILRB1 binding of all tested RIFINs, and abolished signaling in a reporter assay. In a supported lipid bilayer NK cell system, RIFIN recruited to the immunological synapse and reduced NK cell activation (perforin mobilization).\",\n      \"method\": \"X-ray crystallography, site-directed mutagenesis, reporter assay, supported lipid bilayer NK cell activation assay\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure with mutagenesis validation and functional assay in the same study; family-level mechanistic finding for LILRB1-binding RIFINs\",\n      \"pmids\": [\"32650338\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"A specific RIFIN was identified as a novel ligand for LILRB2 (another inhibitory receptor that normally recognizes HLA class I). LILRB2 domain 3 was involved in RIFIN binding, distinct from domains 1 and 2 that bind HLA class I. This was established using a RIFIN expression library screen.\",\n      \"method\": \"RIFIN expression library screen, receptor binding assays, domain mapping\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single-lab screen identifying a specific (unnamed here) RIFIN as LILRB2 ligand; not specific to PF3D7_0100200\",\n      \"pmids\": [\"33647792\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"Promoter titration experiments showed that var, rifin, stevor, and Pfmc-2TM gene families share a common limiting titratable activation factor; episomal overexpression of a rifin promoter caused downregulation not only of rif genes but also of var, stevor, and Pfmc-2TM families. Transcriptionally active promoters from different families co-localized within the same subnuclear expression site.\",\n      \"method\": \"Promoter titration by episomal transfection, quantitative RT-PCR, nuclear co-localization assays\",\n      \"journal\": \"Molecular microbiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic epistasis/promoter competition experiment with multiple gene families; establishes shared transcriptional regulation mechanism for the rif family including PF3D7_0100200\",\n      \"pmids\": [\"19708920\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"The C-terminal domain of a P. falciparum variant antigen rifin prevented GFP export when fused to a KAHRP-like N-terminus in P. berghei, while a PfEMP1 C-terminus allowed export to the erythrocyte surface. This demonstrates that the RIFIN C-terminus contains a domain that blocks export beyond the parasitophorous vacuole.\",\n      \"method\": \"GFP fusion constructs, live-cell fluorescence microscopy in P. berghei transfectants\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single construct experiment in P. berghei; identifies a functional role for the RIFIN C-terminus in restricting export, but not specific to PF3D7_0100200\",\n      \"pmids\": [\"20419102\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}, {\"species\": \"Plasmodium berghei\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Topological studies using confocal and immunoelectron microscopy showed that the semi-conserved N-terminal region of A-type RIFINs is exposed at the erythrocyte surface. At Maurer's clefts, the semi-conserved N-terminal region and variable stretch of RIFINs face the lumen. These results challenge the two-transmembrane topology model, suggesting only one hydrophobic region spans the membrane.\",\n      \"method\": \"Confocal microscopy, immunoelectron microscopy, selective membrane permeabilization, immunoblotting\",\n      \"journal\": \"Malaria journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal imaging methods; family-level topology finding for RIFIN proteins broadly\",\n      \"pmids\": [\"26173856\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"In vitro membrane integration assay using N-linked glycosylation as a topology reporter showed that for RIFIN proteins (three members tested), transmembrane segments TM1 and TM3 integrate into the ER membrane, with overall Ncyt-Ccyt topology. The segment predicted as TM2 was translocated to the ER lumen rather than remaining in the membrane.\",\n      \"method\": \"In vitro N-linked glycosylation topology assay in ER membrane system\",\n      \"journal\": \"The FEBS journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro reconstitution-based topology assay with multiple RIFIN members; finding applies to RIFIN family broadly, not PF3D7_0100200 specifically tested\",\n      \"pmids\": [\"31821735\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"The export of RIFIN (a PEXEL-positive protein) from the ER was decreased by expression of an inactive mutant of PfRab1b or PfArf1 GTPase, indicating that the sequential action of PfArf1 and PfRab1b regulates RIFIN export from the ER. This is distinct from the PfArf1-only pathway used by the PEXEL-negative protein PfAK2.\",\n      \"method\": \"Co-immunoprecipitation, dominant-negative mutant expression, GFP-fusion trafficking assays, indirect immunofluorescence\",\n      \"journal\": \"Frontiers in cellular and infection microbiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic dominant-negative approach with specific trafficking readout; family-level finding for PEXEL-positive RIFINs, not PF3D7_0100200 specifically\",\n      \"pmids\": [\"33604307\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"A chromodomain-containing protein (PfCDP) that binds H3K9me3 was shown to repress rifin gene expression. Conditional deletion of the chromodomain gene led to selective upregulation of a subset of rifin and var genes and promoted RBC rosette formation, establishing an epigenetic mechanism for RIFIN expression control.\",\n      \"method\": \"DiCre-LoxP conditional knockout, ChIP, RT-PCR, rosetting assays\",\n      \"journal\": \"Journal of molecular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — conditional genetic knockout with defined transcriptional and functional phenotype; establishes epigenetic regulation of rifin subset, not PF3D7_0100200 specifically\",\n      \"pmids\": [\"35460670\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"PfBDP7 (a bromodomain protein) and PfBDP1 associate with heterochromatic regions across the gene body of all VSA families, including rifin genes, in early schizonts. Conditional knockdown of PfBDP7 or PfBDP1 de-repressed VSA expression including RIFINs at mRNA and protein levels, identifying these bromodomain proteins as silencers of rifin heterochromatin.\",\n      \"method\": \"ChIP-seq, conditional knockdown, RT-PCR, western blot\",\n      \"journal\": \"Frontiers in cell and developmental biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ChIP-seq with conditional knockdown and defined transcriptional phenotype; family-level finding for rifin silencing, not PF3D7_0100200 specifically\",\n      \"pmids\": [\"35493110\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Crystal and cryo-EM structures of multiple RIFINs in complex with LAIR1 revealed that RIFINs bind LAIR1 through a hydrophobic, membrane-distal region (the V2 domain) in a one-to-one fashion, and that RIFIN-binding sites overlap with collagen-binding sites on LAIR1. Two different RIFINs engage similar LAIR1 binding sites with different angles.\",\n      \"method\": \"X-ray crystallography, cryo-EM, surface plasmon resonance, negative-stain EM\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — multiple crystal structures with functional validation; mechanistic basis for LAIR1-RIFIN interaction established with high resolution structural data\",\n      \"pmids\": [\"34433057\", \"34244481\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"A clade of RIFINs binds to the inhibitory receptor KIR2DL1 more strongly than the natural human ligand MHC class I, mediating inhibitory signaling and suppressing KIR2DL1-expressing NK cell activation. The same RIFIN clade also binds the activating receptor KIR2DS1 (which shares the RIFIN-binding surface), resulting in NK cell activation. Structural basis for KIR2DL1-RIFIN binding was revealed.\",\n      \"method\": \"Receptor binding assays, NK cell activation assays, structural analysis, field strain characterization\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — functional binding and NK cell activation assays combined with structural data; establishes dual inhibitory/activating receptor engagement by RIFIN clade\",\n      \"pmids\": [\"40500441\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"current_model\": \"PF3D7_0100200 is a member of the RIFIN family of clonally variant, PEXEL-containing proteins exported from P. falciparum to the surface of infected erythrocytes via Plasmepsin V-mediated PEXEL cleavage, sequential PfArf1/PfRab1b-regulated ER export, and trafficking through Maurer's clefts; at the erythrocyte surface, RIFINs (with A-type topology of one transmembrane span, Ncyt-Ccyt) mediate rosetting by binding uninfected RBCs preferentially of blood group A, and a subset directly engages inhibitory immune receptors (LILRB1, LILRB2, LAIR1, KIR2DL1) to suppress NK cell and B cell activation, mimicking MHC class I binding mode, while their expression is epigenetically silenced by PfBDP1/PfBDP7 bromodomain proteins and a chromodomain protein (PfCDP) acting through H3K9me3-marked heterochromatin; no mechanistic experiment has been reported for PF3D7_0100200 individually as distinct from other RIFIN family members.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PF3D7_0100200 is a member of the RIFIN family of clonally variant surface antigens of Plasmodium falciparum, and the available corpus establishes nothing about PF3D7_0100200 individually beyond its membership in this family; all mechanistic evidence is drawn at the family level or from sibling RIFIN paralogs [#0, #1]. As a PEXEL-containing RIFIN, PF3D7_0100200 is expected to be exported to the infected-erythrocyte surface through a pathway in which Plasmepsin V cleaves the N-terminal PEXEL motif in the ER [#5], sequential action of the PfArf1 and PfRab1b GTPases drives ER exit [#14], and trafficking proceeds through Maurer's clefts to the erythrocyte surface [#0, #1]. RIFIN proteins adopt a single-membrane-spanning Ncyt-Ccyt topology in which the semi-conserved N-terminal region is displayed at the erythrocyte surface [#12, #13]. At the surface, RIFINs act as adhesins that mediate rosetting by binding uninfected red cells, preferentially of blood group A [#6], and a functional subset engages host inhibitory immune receptors — LILRB1, LAIR1, LILRB2 and KIR2DL1 — through a mode that mimics MHC class I recognition, suppressing NK and B cell activation as an immune-evasion strategy [#7, #8, #17, #18]. Family-wide rifin expression is controlled at the level of mutually exclusive transcription and H3K9me3-marked heterochromatin, with a shared limiting activation factor [#10] and silencing enforced by the bromodomain proteins PfBDP1/PfBDP7 and a chromodomain protein PfCDP [#15, #16]. Whether PF3D7_0100200 itself adopts any specific subtype, rosetting, or receptor-binding activity has not been experimentally addressed in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 1999,\n      \"claim\": \"Establishing that RIFINs are surface-exposed clonally variant antigens defined the family — to which PF3D7_0100200 belongs — as a candidate mediator of host-parasite interaction rather than an internal parasite protein.\",\n      \"evidence\": \"Surface radioiodination, immunoprecipitation, trypsin treatment and agglutination assays on parasitized RBCs, plus rif multigene family characterization\",\n      \"pmids\": [\"10562315\", \"10430943\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No data specific to PF3D7_0100200\", \"Surface exposure shown for representative family members, not this gene\", \"No function assigned at this stage\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Distinguishing A-type (surface-transported) from B-type (parasite-retained) RIFINs partitioned the family functionally, but PF3D7_0100200's subtype was not individually confirmed.\",\n      \"evidence\": \"Indirect immunofluorescence and confocal microscopy of specific RIFIN variants\",\n      \"pmids\": [\"17719658\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Subtype of PF3D7_0100200 not determined\", \"Localization shown for representative members only\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2004,\n      \"claim\": \"Mapping RIFIN trafficking to a shared vesicular pathway with PfEMP1 and Pf332 placed RIFIN export in the context of the broader variant-antigen delivery machinery.\",\n      \"evidence\": \"Immunofluorescence with RIFIN/PfEMP1 antibodies, BODIPY-ceramide lipid staining and vesicle tracking\",\n      \"pmids\": [\"14668007\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Family-level pathway, not PF3D7_0100200-specific\", \"Molecular vesicle machinery not resolved\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2006,\n      \"claim\": \"Identifying the RIFIN C-terminal domain as an export brake beyond Maurer's clefts, using a sibling paralog (PFI0050c), defined the sequence determinants of surface delivery for the family.\",\n      \"evidence\": \"Internal GFP-tagging, live-cell microscopy, selective permeabilization, Brefeldin A treatment in P. falciparum 3D7\",\n      \"pmids\": [\"17014697\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Performed on PFI0050c, not PF3D7_0100200\", \"Single construct; GFP internal tag may perturb trafficking\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"3D7\"}]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"A cross-species GFP-fusion assay confirmed the RIFIN C-terminus autonomously blocks export beyond the parasitophorous vacuole, generalizing the export-restriction determinant.\",\n      \"evidence\": \"GFP fusion constructs and live-cell microscopy in P. berghei transfectants\",\n      \"pmids\": [\"20419102\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Heterologous P. berghei system\", \"Not tested for PF3D7_0100200\", \"Single construct experiment\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}, {\"species\": \"Plasmodium berghei\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Promoter titration revealed that rifin, var, stevor and Pfmc-2TM families compete for a shared limiting activation factor and co-localize at a single subnuclear expression site, explaining mutually exclusive variant-antigen expression that governs PF3D7_0100200 transcription.\",\n      \"evidence\": \"Episomal promoter titration, quantitative RT-PCR and nuclear co-localization assays\",\n      \"pmids\": [\"19708920\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Identity of the limiting factor not determined\", \"Family-level; PF3D7_0100200 not tracked individually\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Demonstrating Plasmepsin V cleavage of the RIFIN PEXEL motif identified the enzymatic step licensing export, applicable to PF3D7_0100200 as a PEXEL-containing member.\",\n      \"evidence\": \"In vitro Plasmepsin V cleavage assay, substrate mutagenesis and N-terminal sequencing\",\n      \"pmids\": [\"23387285\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"PF3D7_0100200 PEXEL not directly assayed\", \"In vitro assay; cellular requirement inferred\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Two advances refined RIFIN topology and assigned an adhesive function: A-type RIFINs display a semi-conserved N-terminal region at the surface (challenging the two-TM model), and surface RIFINs bind uninfected blood group A RBCs to form rosettes.\",\n      \"evidence\": \"Confocal/immunoelectron microscopy with selective permeabilization; rosetting and blood group-specific binding assays with antibody blocking and flow cytometry\",\n      \"pmids\": [\"26173856\", \"25751816\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Rosetting shown for family/representative members, not PF3D7_0100200\", \"RBC receptor for rosetting not molecularly defined here\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Discovering that a subset of RIFINs binds inhibitory receptors LILRB1 and LAIR1 and suppresses B and NK cell activation established direct immune evasion as a RIFIN function.\",\n      \"evidence\": \"Receptor binding assays, B cell and NK cell activation reporters, flow cytometry of patient-isolated infected erythrocytes\",\n      \"pmids\": [\"29186116\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Only a subset of RIFINs binds; PF3D7_0100200 not confirmed as a binder\", \"Receptor repertoire of PF3D7_0100200 unknown\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"In vitro ER-membrane integration assays resolved RIFIN topology to a single spanning arrangement (TM1/TM3 integrate, predicted TM2 translocates), with Ncyt-Ccyt orientation, defining how the ectodomain is displayed.\",\n      \"evidence\": \"In vitro N-linked glycosylation topology reporter assay in an ER membrane system with three RIFIN members\",\n      \"pmids\": [\"31821735\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"PF3D7_0100200 not among the three members tested\", \"In vitro system; native surface topology inferred\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"The RIFIN–LILRB1 crystal structure showed RIFINs mimic the MHC class I binding mode, and a single mutation abolished binding and inhibitory signaling, providing the structural logic of receptor subversion.\",\n      \"evidence\": \"X-ray crystallography, site-directed mutagenesis, reporter assay and supported lipid bilayer NK cell activation assay\",\n      \"pmids\": [\"32650338\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structure from a LILRB1-binding RIFIN, not PF3D7_0100200\", \"Does not establish PF3D7_0100200 as a LILRB1 ligand\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Three advances broadened the inhibitory-receptor map and its structural basis: RIFINs were identified as LILRB2 (domain 3) ligands, LAIR1 complexes were solved showing V2-domain engagement overlapping the collagen-binding site, and PfRab1b/PfArf1 GTPases were shown to sequentially regulate PEXEL-positive RIFIN ER export.\",\n      \"evidence\": \"RIFIN expression library screen and domain mapping; X-ray/cryo-EM/SPR of RIFIN–LAIR1 complexes; dominant-negative GTPase expression with GFP-fusion trafficking and Co-IP\",\n      \"pmids\": [\"33647792\", \"34433057\", \"34244481\", \"33604307\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Specific RIFINs studied are not PF3D7_0100200\", \"LILRB2 finding is a single-lab screen (Low confidence)\", \"Export regulators shown at family level\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Conditional genetics identified the epigenetic silencers of rifin heterochromatin — a H3K9me3-binding chromodomain protein PfCDP and the bromodomain proteins PfBDP1/PfBDP7 — whose loss de-represses rifin/VSA expression and promotes rosetting.\",\n      \"evidence\": \"DiCre-LoxP and conditional knockdown, ChIP/ChIP-seq, RT-PCR, western blot and rosetting assays\",\n      \"pmids\": [\"35460670\", \"35493110\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Regulation shown across rifin subsets/VSA families, not PF3D7_0100200 specifically\", \"Whether PF3D7_0100200 is among the de-repressed loci not stated\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"A RIFIN clade was shown to engage the paired KIR2DL1/KIR2DS1 receptors — binding inhibitory KIR2DL1 more strongly than MHC class I to suppress NK cells while also triggering activation via KIR2DS1 — revealing dual, opposing immune outcomes from a shared binding surface.\",\n      \"evidence\": \"Receptor binding assays, NK cell activation assays, structural analysis and field strain characterization\",\n      \"pmids\": [\"40500441\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Clade-level finding; PF3D7_0100200 membership in this clade not established\", \"In vivo consequence of the inhibitory/activating balance not resolved\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"No experiment has characterized PF3D7_0100200 as an individual protein — its RIFIN subtype, whether it is exported to the erythrocyte surface, and whether it mediates rosetting or binds any specific inhibitory receptor all remain unknown.\",\n      \"evidence\": \"No PF3D7_0100200-specific study present in the corpus; all findings are family-level or from sibling paralogs\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"PF3D7_0100200 subtype (A vs B) undetermined\", \"No direct evidence of surface localization or ligand binding for this gene\", \"No knockout/expression phenotype for PF3D7_0100200\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0050839\", \"supporting_discovery_ids\": [6, 7, 8, 17, 18]},\n      {\"term_id\": \"GO:0038023\", \"supporting_discovery_ids\": [7, 8, 9, 17, 18]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0009986\", \"supporting_discovery_ids\": [0, 1, 12]},\n      {\"term_id\": \"GO:0020036\", \"supporting_discovery_ids\": [2, 3, 4, 12]},\n      {\"term_id\": \"GO:0005789\", \"supporting_discovery_ids\": [5, 13, 14]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0046903\", \"supporting_discovery_ids\": [4, 5, 14]},\n      {\"term_id\": \"GO:0051701\", \"supporting_discovery_ids\": [7, 8, 17, 18]},\n      {\"term_id\": \"GO:0006338\", \"supporting_discovery_ids\": [10, 15, 16]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\n      \"LILRB1 (host inhibitory receptor; bound by a RIFIN subset, family-level)\",\n      \"LAIR1 (host inhibitory receptor; RIFIN V2 domain, family-level)\",\n      \"LILRB2 (host inhibitory receptor domain 3; family-level)\",\n      \"KIR2DL1/KIR2DS1 (host paired receptors; RIFIN clade, family-level)\",\n      \"Plasmepsin V (PEXEL-cleaving protease acting on RIFIN export signal, family-level)\",\n      \"PfArf1 / PfRab1b (GTPases regulating RIFIN ER export, family-level)\",\n      \"PfBDP1 / PfBDP7 / PfCDP (epigenetic silencers of rifin loci, family-level)\"\n    ],\n    \"other_free_text\": [\n      \"No mechanistic experiment has been reported for PF3D7_0100200 as an individual gene; all cited findings are established at the RIFIN family level or in sibling paralogs (e.g. PFI0050c).\",\n      \"RIFINs adopt a single-transmembrane Ncyt-Ccyt topology with the semi-conserved N-terminal region surface-exposed [#12, #13].\",\n      \"RIFIN-mediated rosetting shows preference for blood group A red cells [#6].\"\n    ]\n  }\n}","audit_flag":null,"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_0100200","name":null,"product":"rifin","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"","evaluation":null}