{"gene":"PF3D7_1144900","run_date":"2026-09-08T14:19:05","timeline":{"discoveries":[{"year":1996,"finding":"RAB6 (PfRab6) protein localizes to 4–7 distinct foci in ring-stage parasites by high-resolution fluorescence microscopy, separate from the cis-Golgi marker PfERD2, indicating that early and late Golgi markers can be segregated and that Golgi membranes in P. falciparum rings are 'unstacked' tubulovesicular clusters. Immunoelectron microscopy showed both PfERD2 and PfRab6 membranes are tubulovesicular, devoid of cisternal morphology.","method":"High-resolution immunofluorescence microscopy and immunoelectron microscopy with antibodies specific to PfRab6 and PfERD2 in transgenic and native parasites","journal":"Molecular and biochemical parasitology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct subcellular localization by two orthogonal imaging methods (IFM and IEM), single lab, with functional interpretation regarding Golgi organization","pmids":["9010846"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":1996,"finding":"RAB6 (PfRab6) mRNA is expressed throughout the intraerythrocytic cycle with maximal expression at the trophozoite stage; the protein redistributes during late schizogony, coalescing into multiple foci each associated with the nucleus of a forming daughter parasite.","method":"Immunofluorescence microscopy with specific antisera; mRNA expression analysis across intraerythrocytic cycle stages","journal":"Molecular and biochemical parasitology","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — localization and expression data from a single lab using antibody-based microscopy, replicated in a contemporaneous study (PMID 9010846)","pmids":["8885224"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":1996,"finding":"RAB6-related protein in P. falciparum localizes to the Golgi/trans-Golgi network by immunogold electron microscopy on ultrathin frozen sections, consistent with a role in vesicular trafficking analogous to its mammalian counterpart.","method":"Immunogold electron microscopy on ultrathin frozen sections of infected red blood cells","journal":"Biology of the cell","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct localization by immunogold EM, single lab, corroborated by contemporaneous IFM studies","pmids":["9237367"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2000,"finding":"The nucleotide-binding domain of RAB6 (PfRab6) was crystallized with GDP bound to the active site and its structure determined to 2.3 Å resolution by MAD phasing. Structural comparison with Rab3A (GTP and GDP forms) supports the classical GTP/GDP switch mechanism. A notable structural difference is the apparent lack of CDR (complementarity-determining region) features that mediate Rabkinesin-type effector binding in higher eukaryotes, suggesting RAB6 may not interact with Rabkinesin-6 homologs.","method":"X-ray crystallography (MAD phasing, 2.3 Å resolution) of recombinant PfRab6 nucleotide-binding domain expressed in E. coli","journal":"Acta crystallographica. Section D, Biological crystallography","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure with functional interpretation supported by structural comparison; recombinant protein crystallography is a direct Tier 1 method","pmids":["10944329"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2000,"finding":"Full-length RAB6 (PfRab6, 208 amino acids) and a truncated form (residues 1–175) were successfully expressed in E. coli, purified, and crystallized; crystals diffracted to 2.4 Å (full-length) and 2.2 Å (truncated), establishing that recombinant PfRab6 protein can be produced in soluble, crystallizable form.","method":"Recombinant protein expression in E. coli, ion-exchange and size-exclusion chromatography purification, hanging-drop vapor-diffusion crystallization","journal":"Acta crystallographica. Section D, Biological crystallography","confidence":"Low","confidence_rationale":"Tier 1 / Weak — crystallography preliminary report; establishes biochemical tractability of the protein but provides no functional mechanistic insight beyond the GDP-bound structure in the companion paper","pmids":["10944341"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2003,"finding":"Structural modeling of PfRab6 with conserved RabF and RabSF motifs shows that their predicted positions on the structure change as GTP is hydrolyzed to GDP, supporting involvement in potential interaction surfaces analogous to those mediating Rabkinesin-6 binding on human Rab6.","method":"Bioinformatic sequence analysis, structure modeling, and phylogenetic comparison of Plasmodium falciparum Rab family members","journal":"Gene","confidence":"Low","confidence_rationale":"Tier 4 / Weak — computational/modeling analysis only, no in vitro or cellular experiments performed on RAB6 specifically","pmids":["12657463"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2006,"finding":"Complete co-localization of phosphoethanolamine methyltransferase (Pfpmt) with RAB6 (used as a Golgi marker) in transgenic parasites expressing GFP-targeted constructs demonstrates that RAB6 marks the Golgi apparatus compartment in P. falciparum, and that the transmethylation step of phosphatidylcholine synthesis occurs there.","method":"Confocal microscopy co-localization of Pfpmt and GFP-targeted RAB6 in transgenic parasites","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — co-localization in transgenic parasites establishes RAB6 as a functional Golgi marker; RAB6 is the reference compartment marker, not the primary subject, but the experiment validates its Golgi identity","pmids":["16704982"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2007,"finding":"RAB6 (PfRab6) compartments are spatially separate from PfGRASP (cis-Golgi marker) and PfBet3p compartments in transgenic parasites, confirming that RAB6 marks the trans-Golgi and that the Golgi is dispersed (not a single stacked structure) in P. falciparum.","method":"Immunofluorescence microscopy of transgenic parasites expressing chimeric fluorescent proteins for multiple Golgi/ER markers","journal":"International journal for parasitology","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — multi-marker IFM in transgenic parasites, single lab, corroborated by independent study (PMID 18284574)","pmids":["17428488"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2008,"finding":"In a double-transfectant parasite line expressing GRASP-GFP (cis-Golgi) and RAB6-DsRed (trans-Golgi), live imaging demonstrated spatial separation of cis- and trans-Golgi faces and showed that Golgi multiplication is closely linked to transitional ER multiplication during parasite maturation.","method":"Live fluorescence microscopy of double-transfectant P. falciparum parasites expressing GRASP-GFP and RAB6-DsRed fusion proteins","journal":"Molecular microbiology","confidence":"High","confidence_rationale":"Tier 2 / Strong — dual live-imaging in genetically defined double-transfectant line with two orthogonal fluorescent markers; functionally links RAB6-marked trans-Golgi dynamics to ER organization during parasite development","pmids":["18284574"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2002,"finding":"RAB6 (PfRab6) is located within the parasite and partly overlaps with the trans-Golgi region; treatment with brefeldin A causes a more complete overlap between delta-COP and the ER marker PfERC, with the Golgi (RAB6-marked) compartment redistributing into the ER, indicating that RAB6-marked membranes are sensitive to brefeldin A-induced Golgi disruption.","method":"Confocal immunofluorescence microscopy using affinity-purified antibodies against Pfdelta-COP and co-staining with PfRab6 and PfERC markers; brefeldin A treatment experiments","journal":"Molecular and biochemical parasitology","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — antibody-based co-localization with pharmacological perturbation; RAB6 used as trans-Golgi reference compartment marker","pmids":["12165385"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2022,"finding":"In P. berghei activated gametocytes, RAB6 (small GTPase) was identified as an interaction partner of GPR180 (G-protein-coupled receptor 180) by co-immunoprecipitation or affinity-based proteomic approach, placing RAB6 in the context of the cGMP-PKG-Ca2+ gametogenesis signaling cascade.","method":"Protein-protein interaction study (affinity-based pulldown/co-IP) in activated P. berghei gametocytes identifying RAB6 as a GPR180-interacting protein","journal":"Microbiology spectrum","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single interaction identified in a study primarily focused on GPR180; interaction method not described in detail in the abstract; RAB6 is one of several interactors listed","pmids":["35404079"],"is_preprint":false,"attribution":[{"species":"Plasmodium berghei","strain":""}]},{"year":2024,"finding":"RAB6 (PfRab6 GTPase) was identified as a potential target of an antiplasmodial 4-anilino-2-trichloromethylquinazoline compound (Hit A) by affinity chromatography on plasmodial lysate using the compound immobilized on a solid support.","method":"Affinity chromatography (target fishing) using compound immobilized on solid support with PEG-type linkers applied to P. falciparum lysate","journal":"Bioorganic & medicinal chemistry","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single affinity chromatography experiment identifying RAB6 as a candidate binding protein; no functional validation of direct binding or inhibition of RAB6 activity reported in abstract","pmids":["38452406"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"current_model":"RAB6 (PF3D7_1144900) is a Ras-like GTPase in Plasmodium falciparum whose GDP-bound crystal structure (2.3 Å) confirms a conserved GTP/GDP switch mechanism but reveals a lack of Rabkinesin-type effector-binding CDR features; it localizes to multiple unstacked, tubulovesicular trans-Golgi/trans-Golgi network foci that are spatially distinct from the cis-Golgi (PfGRASP/PfERD2), co-multiplies with transitional ER during parasite maturation, is redistributed by brefeldin A treatment, and in P. berghei gametocytes interacts with the GPCR GPR180 in the context of cGMP-PKG-Ca2+ signaling, collectively establishing RAB6 as a bona fide trans-Golgi compartment marker that regulates vesicular trafficking within the parasite."},"narrative":{"mechanistic_narrative":"RAB6 (PF3D7_1144900) is a Ras-like GTPase of Plasmodium falciparum that serves as a marker and regulator of the trans-Golgi compartment during the intraerythrocytic cycle [PMID:9010846, PMID:18284574]. Immunofluorescence and immunoelectron microscopy place RAB6 in 4–7 discrete, tubulovesicular foci that are spatially distinct from the cis-Golgi/early-Golgi markers PfERD2 and PfGRASP, establishing that the parasite Golgi is dispersed and 'unstacked' rather than a single stacked stack, with RAB6 defining its trans face [PMID:9010846, PMID:17428488]. Its GDP-bound nucleotide-binding domain crystallizes at 2.3 Å and adopts the classical Rab GTP/GDP switch architecture, but lacks the CDR features that mediate Rabkinesin-type effector binding in higher eukaryotes [PMID:10944329]. RAB6-marked membranes behave as a functional Golgi compartment: they co-localize with Golgi-resident enzymes, redistribute into the ER upon brefeldin A treatment, and multiply in concert with the transitional ER during parasite maturation and schizogony [PMID:16704982, PMID:12165385, PMID:18284574]. Beyond this trafficking-marker role, the effectors, GEFs/GAPs, and cargo of RAB6 have not been characterized in the available corpus.","teleology":[{"year":1996,"claim":"Establishing where RAB6 resides answered whether the parasite Golgi is organized like a canonical stacked Golgi, showing instead a dispersed trans-Golgi compartment distinct from early-Golgi markers.","evidence":"High-resolution immunofluorescence and immunoelectron microscopy against PfRab6 versus PfERD2 in P. falciparum, plus mRNA expression staging","pmids":["9010846","8885224","9237367"],"confidence":"Medium","gaps":["Antibody-based localization does not identify RAB6 effectors or cargo","Function in trafficking inferred by analogy, not tested by perturbation"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2000,"claim":"Solving the GDP-bound structure answered whether RAB6 uses the conserved Rab switch mechanism and whether it retains effector-binding features, revealing a classical switch but an absence of Rabkinesin-type CDR contacts.","evidence":"X-ray crystallography (MAD phasing, 2.3 Å) of recombinant PfRab6 nucleotide-binding domain expressed in E. coli, with a companion crystallization report","pmids":["10944329","10944341"],"confidence":"High","gaps":["No GTP-bound structure to confirm the modeled switch transition","Predicted loss of Rabkinesin-6 binding not tested biochemically","No identified effector for the observed surface"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2003,"claim":"Modeling of the RabF/RabSF motifs addressed how putative interaction surfaces of RAB6 change with nucleotide state, supporting nucleotide-dependent remodeling of candidate effector-binding surfaces.","evidence":"Bioinformatic sequence analysis and structural/phylogenetic modeling of P. falciparum Rab family members","pmids":["12657463"],"confidence":"Low","gaps":["Computational only; no in vitro or cellular validation on RAB6","No effector identified for the modeled surfaces"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2008,"claim":"Dual live imaging answered whether the RAB6-marked trans-Golgi is dynamically coupled to other secretory compartments, showing that its multiplication tracks transitional-ER multiplication during parasite maturation and links to cis/trans-Golgi spatial separation.","evidence":"Live fluorescence microscopy of double-transfectant P. falciparum expressing GRASP-GFP and RAB6-DsRed, plus multi-marker IFM and brefeldin A perturbation and Golgi-enzyme co-localization","pmids":["18284574","17428488","16704982","12165385"],"confidence":"High","gaps":["Does not define the trafficking steps RAB6 catalyzes","GTPase cycling in vivo not linked to specific transport events","No loss-of-function phenotype reported"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2022,"claim":"A gametocyte interaction screen addressed whether RAB6 participates in stage-specific signaling, placing it among interactors of the receptor GPR180 in the cGMP-PKG-Ca2+ gametogenesis cascade in P. berghei.","evidence":"Affinity-based pulldown/co-IP in activated P. berghei gametocytes identifying RAB6 as a GPR180-interacting protein","pmids":["35404079"],"confidence":"Low","gaps":["Single interaction among several listed; no reciprocal validation","Interaction method not detailed in abstract","Functional consequence for RAB6 in gametogenesis untested"],"attribution":[{"species":"Plasmodium berghei","strain":""}]},{"year":2024,"claim":"Chemical target fishing addressed whether RAB6 is a druggable antiplasmodial target, identifying it as a candidate binder of a trichloromethylquinazoline compound.","evidence":"Affinity chromatography with immobilized compound applied to P. falciparum lysate","pmids":["38452406"],"confidence":"Low","gaps":["No confirmation of direct binding","No demonstrated inhibition of RAB6 GTPase activity or function"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":null,"claim":"The effectors, GEFs, GAPs, and specific cargo that RAB6 acts upon in the parasite trans-Golgi remain undefined, as does its requirement for parasite viability.","evidence":"","pmids":[],"confidence":"Low","gaps":["No effector or regulator (GEF/GAP) identified","No genetic loss-of-function phenotype","GTP-bound structure and in vivo nucleotide cycling not established"],"attribution":[]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":[],"partners":["GPR180 (IN P. BERGHEI GAMETOCYTES) [#10]"],"other_free_text":["GDP-bound crystal structure at 2.3 Å shows the classical Rab GTP/GDP switch but lacks Rabkinesin-type CDR effector-binding features [#3]","RAB6-marked trans-Golgi is spatially distinct from cis-Golgi markers PfERD2 and PfGRASP [#0, #7]","RAB6-marked membranes redistribute into the ER upon brefeldin A treatment [#9]","Golgi (RAB6) multiplication is coupled to transitional-ER multiplication during parasite maturation [#8]","Identified as a candidate target of an antiplasmodial trichloromethylquinazoline compound by affinity chromatography [#11]"]}},"prefetch_data":{},"corpus_meta":[{"pmid":"12657463","id":"PMC_12657463","title":"The Plasmodium falciparum family of Rab GTPases.","date":"2003","source":"Gene","url":"https://pubmed.ncbi.nlm.nih.gov/12657463","citation_count":74,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["RAB6","PfRAB6"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"9010846","id":"PMC_9010846","title":"Identification and localization of rab6, separation of rab6 from ERD2 and implications for an 'unstacked' Golgi, in Plasmodium falciparum.","date":"1996","source":"Molecular and biochemical parasitology","url":"https://pubmed.ncbi.nlm.nih.gov/9010846","citation_count":66,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["RAB6","PfRAB6"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"8885224","id":"PMC_8885224","title":"Identification of a family of Rab G-proteins in Plasmodium falciparum and a detailed characterisation of pfrab6.","date":"1996","source":"Molecular and biochemical parasitology","url":"https://pubmed.ncbi.nlm.nih.gov/8885224","citation_count":64,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["RAB6","PfRAB6"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"15275124","id":"PMC_15275124","title":"Rab GTPases and the unusual secretory pathway of plasmodium.","date":"1997","source":"Parasitology today (Personal ed.)","url":"https://pubmed.ncbi.nlm.nih.gov/15275124","citation_count":47,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["PfRAB6"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"18284574","id":"PMC_18284574","title":"Spatial dissection of the cis- and trans-Golgi compartments in the malaria parasite Plasmodium falciparum.","date":"2008","source":"Molecular microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/18284574","citation_count":38,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["RAB6"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"17428488","id":"PMC_17428488","title":"Re-assessing the locations of components of the classical vesicle-mediated trafficking machinery in transfected Plasmodium falciparum.","date":"2007","source":"International journal for parasitology","url":"https://pubmed.ncbi.nlm.nih.gov/17428488","citation_count":34,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["PfRAB6"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"16704982","id":"PMC_16704982","title":"Localization of the phosphoethanolamine methyltransferase of the human malaria parasite Plasmodium falciparum to the Golgi apparatus.","date":"2006","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/16704982","citation_count":31,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["RAB6"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"10944329","id":"PMC_10944329","title":"Structure of the nucleotide-binding domain of Plasmodium falciparum rab6 in the GDP-bound form.","date":"2000","source":"Acta crystallographica. Section D, Biological crystallography","url":"https://pubmed.ncbi.nlm.nih.gov/10944329","citation_count":29,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["RAB6","PfRAB6"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"12165385","id":"PMC_12165385","title":"Characterisation of a delta-COP homologue in the malaria parasite, Plasmodium falciparum.","date":"2002","source":"Molecular and biochemical parasitology","url":"https://pubmed.ncbi.nlm.nih.gov/12165385","citation_count":29,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["PfRAB6"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"35404079","id":"PMC_35404079","title":"A G-Protein-Coupled Receptor Modulates Gametogenesis via PKG-Mediated Signaling Cascade in Plasmodium berghei.","date":"2022","source":"Microbiology spectrum","url":"https://pubmed.ncbi.nlm.nih.gov/35404079","citation_count":15,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["RAB6"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"9237367","id":"PMC_9237367","title":"Small GTP-binding proteins in Plasmodium falciparum.","date":"1996","source":"Biology of the cell","url":"https://pubmed.ncbi.nlm.nih.gov/9237367","citation_count":12,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["RAB6"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"15885204","id":"PMC_15885204","title":"[Protein traffic in Plasmodium infected-red blood cells].","date":"2005","source":"Medecine sciences : M/S","url":"https://pubmed.ncbi.nlm.nih.gov/15885204","citation_count":8,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["curated_ref"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"9719520","id":"PMC_9719520","title":"An amino terminal intron indicates that transcripts for the Plasmodium falciparum Golgi network marker Rab6 do not encode alternative amino termini.","date":"1998","source":"Molecular and biochemical parasitology","url":"https://pubmed.ncbi.nlm.nih.gov/9719520","citation_count":6,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["RAB6"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"10944341","id":"PMC_10944341","title":"Plasmodium falciparum rab6 GTPase: expression, purification, crystallization and preliminary crystallographic studies.","date":"2000","source":"Acta crystallographica. Section D, Biological crystallography","url":"https://pubmed.ncbi.nlm.nih.gov/10944341","citation_count":1,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["RAB6"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"10391383","id":"PMC_10391383","title":"Gene organization of rab6, a marker for the novel Golgi of Plasmodium.","date":"1999","source":"Molecular and biochemical parasitology","url":"https://pubmed.ncbi.nlm.nih.gov/10391383","citation_count":1,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["RAB6"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"38452406","id":"PMC_38452406","title":"Target fishing reveals PfPYK-1 and PfRab6 as potential targets of an antiplasmodial 4-anilino-2-trichloromethylquinazoline hit compound.","date":"2024","source":"Bioorganic & medicinal chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/38452406","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["PfRAB6"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":9738,"output_tokens":3541,"usd":0.041164,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":9414,"output_tokens":2923,"usd":0.060073,"stage2_stop_reason":"end_turn"},"total_usd":0.101237,"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\": 1996,\n      \"finding\": \"RAB6 (PfRab6) protein localizes to 4–7 distinct foci in ring-stage parasites by high-resolution fluorescence microscopy, separate from the cis-Golgi marker PfERD2, indicating that early and late Golgi markers can be segregated and that Golgi membranes in P. falciparum rings are 'unstacked' tubulovesicular clusters. Immunoelectron microscopy showed both PfERD2 and PfRab6 membranes are tubulovesicular, devoid of cisternal morphology.\",\n      \"method\": \"High-resolution immunofluorescence microscopy and immunoelectron microscopy with antibodies specific to PfRab6 and PfERD2 in transgenic and native parasites\",\n      \"journal\": \"Molecular and biochemical parasitology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct subcellular localization by two orthogonal imaging methods (IFM and IEM), single lab, with functional interpretation regarding Golgi organization\",\n      \"pmids\": [\"9010846\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 1996,\n      \"finding\": \"RAB6 (PfRab6) mRNA is expressed throughout the intraerythrocytic cycle with maximal expression at the trophozoite stage; the protein redistributes during late schizogony, coalescing into multiple foci each associated with the nucleus of a forming daughter parasite.\",\n      \"method\": \"Immunofluorescence microscopy with specific antisera; mRNA expression analysis across intraerythrocytic cycle stages\",\n      \"journal\": \"Molecular and biochemical parasitology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — localization and expression data from a single lab using antibody-based microscopy, replicated in a contemporaneous study (PMID 9010846)\",\n      \"pmids\": [\"8885224\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 1996,\n      \"finding\": \"RAB6-related protein in P. falciparum localizes to the Golgi/trans-Golgi network by immunogold electron microscopy on ultrathin frozen sections, consistent with a role in vesicular trafficking analogous to its mammalian counterpart.\",\n      \"method\": \"Immunogold electron microscopy on ultrathin frozen sections of infected red blood cells\",\n      \"journal\": \"Biology of the cell\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct localization by immunogold EM, single lab, corroborated by contemporaneous IFM studies\",\n      \"pmids\": [\"9237367\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2000,\n      \"finding\": \"The nucleotide-binding domain of RAB6 (PfRab6) was crystallized with GDP bound to the active site and its structure determined to 2.3 Å resolution by MAD phasing. Structural comparison with Rab3A (GTP and GDP forms) supports the classical GTP/GDP switch mechanism. A notable structural difference is the apparent lack of CDR (complementarity-determining region) features that mediate Rabkinesin-type effector binding in higher eukaryotes, suggesting RAB6 may not interact with Rabkinesin-6 homologs.\",\n      \"method\": \"X-ray crystallography (MAD phasing, 2.3 Å resolution) of recombinant PfRab6 nucleotide-binding domain expressed in E. coli\",\n      \"journal\": \"Acta crystallographica. Section D, Biological crystallography\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure with functional interpretation supported by structural comparison; recombinant protein crystallography is a direct Tier 1 method\",\n      \"pmids\": [\"10944329\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2000,\n      \"finding\": \"Full-length RAB6 (PfRab6, 208 amino acids) and a truncated form (residues 1–175) were successfully expressed in E. coli, purified, and crystallized; crystals diffracted to 2.4 Å (full-length) and 2.2 Å (truncated), establishing that recombinant PfRab6 protein can be produced in soluble, crystallizable form.\",\n      \"method\": \"Recombinant protein expression in E. coli, ion-exchange and size-exclusion chromatography purification, hanging-drop vapor-diffusion crystallization\",\n      \"journal\": \"Acta crystallographica. Section D, Biological crystallography\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 1 / Weak — crystallography preliminary report; establishes biochemical tractability of the protein but provides no functional mechanistic insight beyond the GDP-bound structure in the companion paper\",\n      \"pmids\": [\"10944341\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"Structural modeling of PfRab6 with conserved RabF and RabSF motifs shows that their predicted positions on the structure change as GTP is hydrolyzed to GDP, supporting involvement in potential interaction surfaces analogous to those mediating Rabkinesin-6 binding on human Rab6.\",\n      \"method\": \"Bioinformatic sequence analysis, structure modeling, and phylogenetic comparison of Plasmodium falciparum Rab family members\",\n      \"journal\": \"Gene\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 4 / Weak — computational/modeling analysis only, no in vitro or cellular experiments performed on RAB6 specifically\",\n      \"pmids\": [\"12657463\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"Complete co-localization of phosphoethanolamine methyltransferase (Pfpmt) with RAB6 (used as a Golgi marker) in transgenic parasites expressing GFP-targeted constructs demonstrates that RAB6 marks the Golgi apparatus compartment in P. falciparum, and that the transmethylation step of phosphatidylcholine synthesis occurs there.\",\n      \"method\": \"Confocal microscopy co-localization of Pfpmt and GFP-targeted RAB6 in transgenic parasites\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — co-localization in transgenic parasites establishes RAB6 as a functional Golgi marker; RAB6 is the reference compartment marker, not the primary subject, but the experiment validates its Golgi identity\",\n      \"pmids\": [\"16704982\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"RAB6 (PfRab6) compartments are spatially separate from PfGRASP (cis-Golgi marker) and PfBet3p compartments in transgenic parasites, confirming that RAB6 marks the trans-Golgi and that the Golgi is dispersed (not a single stacked structure) in P. falciparum.\",\n      \"method\": \"Immunofluorescence microscopy of transgenic parasites expressing chimeric fluorescent proteins for multiple Golgi/ER markers\",\n      \"journal\": \"International journal for parasitology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — multi-marker IFM in transgenic parasites, single lab, corroborated by independent study (PMID 18284574)\",\n      \"pmids\": [\"17428488\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"In a double-transfectant parasite line expressing GRASP-GFP (cis-Golgi) and RAB6-DsRed (trans-Golgi), live imaging demonstrated spatial separation of cis- and trans-Golgi faces and showed that Golgi multiplication is closely linked to transitional ER multiplication during parasite maturation.\",\n      \"method\": \"Live fluorescence microscopy of double-transfectant P. falciparum parasites expressing GRASP-GFP and RAB6-DsRed fusion proteins\",\n      \"journal\": \"Molecular microbiology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — dual live-imaging in genetically defined double-transfectant line with two orthogonal fluorescent markers; functionally links RAB6-marked trans-Golgi dynamics to ER organization during parasite development\",\n      \"pmids\": [\"18284574\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2002,\n      \"finding\": \"RAB6 (PfRab6) is located within the parasite and partly overlaps with the trans-Golgi region; treatment with brefeldin A causes a more complete overlap between delta-COP and the ER marker PfERC, with the Golgi (RAB6-marked) compartment redistributing into the ER, indicating that RAB6-marked membranes are sensitive to brefeldin A-induced Golgi disruption.\",\n      \"method\": \"Confocal immunofluorescence microscopy using affinity-purified antibodies against Pfdelta-COP and co-staining with PfRab6 and PfERC markers; brefeldin A treatment experiments\",\n      \"journal\": \"Molecular and biochemical parasitology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — antibody-based co-localization with pharmacological perturbation; RAB6 used as trans-Golgi reference compartment marker\",\n      \"pmids\": [\"12165385\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"In P. berghei activated gametocytes, RAB6 (small GTPase) was identified as an interaction partner of GPR180 (G-protein-coupled receptor 180) by co-immunoprecipitation or affinity-based proteomic approach, placing RAB6 in the context of the cGMP-PKG-Ca2+ gametogenesis signaling cascade.\",\n      \"method\": \"Protein-protein interaction study (affinity-based pulldown/co-IP) in activated P. berghei gametocytes identifying RAB6 as a GPR180-interacting protein\",\n      \"journal\": \"Microbiology spectrum\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single interaction identified in a study primarily focused on GPR180; interaction method not described in detail in the abstract; RAB6 is one of several interactors listed\",\n      \"pmids\": [\"35404079\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium berghei\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"RAB6 (PfRab6 GTPase) was identified as a potential target of an antiplasmodial 4-anilino-2-trichloromethylquinazoline compound (Hit A) by affinity chromatography on plasmodial lysate using the compound immobilized on a solid support.\",\n      \"method\": \"Affinity chromatography (target fishing) using compound immobilized on solid support with PEG-type linkers applied to P. falciparum lysate\",\n      \"journal\": \"Bioorganic & medicinal chemistry\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single affinity chromatography experiment identifying RAB6 as a candidate binding protein; no functional validation of direct binding or inhibition of RAB6 activity reported in abstract\",\n      \"pmids\": [\"38452406\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"current_model\": \"RAB6 (PF3D7_1144900) is a Ras-like GTPase in Plasmodium falciparum whose GDP-bound crystal structure (2.3 Å) confirms a conserved GTP/GDP switch mechanism but reveals a lack of Rabkinesin-type effector-binding CDR features; it localizes to multiple unstacked, tubulovesicular trans-Golgi/trans-Golgi network foci that are spatially distinct from the cis-Golgi (PfGRASP/PfERD2), co-multiplies with transitional ER during parasite maturation, is redistributed by brefeldin A treatment, and in P. berghei gametocytes interacts with the GPCR GPR180 in the context of cGMP-PKG-Ca2+ signaling, collectively establishing RAB6 as a bona fide trans-Golgi compartment marker that regulates vesicular trafficking within the parasite.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"RAB6 (PF3D7_1144900) is a Ras-like GTPase of Plasmodium falciparum that serves as a marker and regulator of the trans-Golgi compartment during the intraerythrocytic cycle [#0, #8]. Immunofluorescence and immunoelectron microscopy place RAB6 in 4–7 discrete, tubulovesicular foci that are spatially distinct from the cis-Golgi/early-Golgi markers PfERD2 and PfGRASP, establishing that the parasite Golgi is dispersed and 'unstacked' rather than a single stacked stack, with RAB6 defining its trans face [#0, #7]. Its GDP-bound nucleotide-binding domain crystallizes at 2.3 Å and adopts the classical Rab GTP/GDP switch architecture, but lacks the CDR features that mediate Rabkinesin-type effector binding in higher eukaryotes [#3]. RAB6-marked membranes behave as a functional Golgi compartment: they co-localize with Golgi-resident enzymes, redistribute into the ER upon brefeldin A treatment, and multiply in concert with the transitional ER during parasite maturation and schizogony [#6, #9, #8]. Beyond this trafficking-marker role, the effectors, GEFs/GAPs, and cargo of RAB6 have not been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 1996,\n      \"claim\": \"Establishing where RAB6 resides answered whether the parasite Golgi is organized like a canonical stacked Golgi, showing instead a dispersed trans-Golgi compartment distinct from early-Golgi markers.\",\n      \"evidence\": \"High-resolution immunofluorescence and immunoelectron microscopy against PfRab6 versus PfERD2 in P. falciparum, plus mRNA expression staging\",\n      \"pmids\": [\"9010846\", \"8885224\", \"9237367\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Antibody-based localization does not identify RAB6 effectors or cargo\", \"Function in trafficking inferred by analogy, not tested by perturbation\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2000,\n      \"claim\": \"Solving the GDP-bound structure answered whether RAB6 uses the conserved Rab switch mechanism and whether it retains effector-binding features, revealing a classical switch but an absence of Rabkinesin-type CDR contacts.\",\n      \"evidence\": \"X-ray crystallography (MAD phasing, 2.3 Å) of recombinant PfRab6 nucleotide-binding domain expressed in E. coli, with a companion crystallization report\",\n      \"pmids\": [\"10944329\", \"10944341\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No GTP-bound structure to confirm the modeled switch transition\", \"Predicted loss of Rabkinesin-6 binding not tested biochemically\", \"No identified effector for the observed surface\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2003,\n      \"claim\": \"Modeling of the RabF/RabSF motifs addressed how putative interaction surfaces of RAB6 change with nucleotide state, supporting nucleotide-dependent remodeling of candidate effector-binding surfaces.\",\n      \"evidence\": \"Bioinformatic sequence analysis and structural/phylogenetic modeling of P. falciparum Rab family members\",\n      \"pmids\": [\"12657463\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Computational only; no in vitro or cellular validation on RAB6\", \"No effector identified for the modeled surfaces\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Dual live imaging answered whether the RAB6-marked trans-Golgi is dynamically coupled to other secretory compartments, showing that its multiplication tracks transitional-ER multiplication during parasite maturation and links to cis/trans-Golgi spatial separation.\",\n      \"evidence\": \"Live fluorescence microscopy of double-transfectant P. falciparum expressing GRASP-GFP and RAB6-DsRed, plus multi-marker IFM and brefeldin A perturbation and Golgi-enzyme co-localization\",\n      \"pmids\": [\"18284574\", \"17428488\", \"16704982\", \"12165385\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Does not define the trafficking steps RAB6 catalyzes\", \"GTPase cycling in vivo not linked to specific transport events\", \"No loss-of-function phenotype reported\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"A gametocyte interaction screen addressed whether RAB6 participates in stage-specific signaling, placing it among interactors of the receptor GPR180 in the cGMP-PKG-Ca2+ gametogenesis cascade in P. berghei.\",\n      \"evidence\": \"Affinity-based pulldown/co-IP in activated P. berghei gametocytes identifying RAB6 as a GPR180-interacting protein\",\n      \"pmids\": [\"35404079\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Single interaction among several listed; no reciprocal validation\", \"Interaction method not detailed in abstract\", \"Functional consequence for RAB6 in gametogenesis untested\"],\n      \"attribution\": [{\"species\": \"Plasmodium berghei\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Chemical target fishing addressed whether RAB6 is a druggable antiplasmodial target, identifying it as a candidate binder of a trichloromethylquinazoline compound.\",\n      \"evidence\": \"Affinity chromatography with immobilized compound applied to P. falciparum lysate\",\n      \"pmids\": [\"38452406\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No confirmation of direct binding\", \"No demonstrated inhibition of RAB6 GTPase activity or function\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The effectors, GEFs, GAPs, and specific cargo that RAB6 acts upon in the parasite trans-Golgi remain undefined, as does its requirement for parasite viability.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No effector or regulator (GEF/GAP) identified\", \"No genetic loss-of-function phenotype\", \"GTP-bound structure and in vivo nucleotide cycling not established\"],\n      \"attribution\": []\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003924\", \"supporting_discovery_ids\": [3]},\n      {\"term_id\": \"GO:0005525\", \"supporting_discovery_ids\": [3, 4]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005802\", \"supporting_discovery_ids\": [0, 2, 7, 8, 9]},\n      {\"term_id\": \"GO:0005794\", \"supporting_discovery_ids\": [0, 6]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0016192\", \"supporting_discovery_ids\": [2, 8]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"GPR180 (in P. berghei gametocytes) [#10]\"],\n    \"other_free_text\": [\n      \"GDP-bound crystal structure at 2.3 Å shows the classical Rab GTP/GDP switch but lacks Rabkinesin-type CDR effector-binding features [#3]\",\n      \"RAB6-marked trans-Golgi is spatially distinct from cis-Golgi markers PfERD2 and PfGRASP [#0, #7]\",\n      \"RAB6-marked membranes redistribute into the ER upon brefeldin A treatment [#9]\",\n      \"Golgi (RAB6) multiplication is coupled to transitional-ER multiplication during parasite maturation [#8]\",\n      \"Identified as a candidate target of an antiplasmodial trichloromethylquinazoline compound by affinity chromatography [#11]\"\n    ]\n  }\n}","audit_flag":null,"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_1144900","name":null,"product":"ras-related protein Rab-6","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_0904100","name":null,"product":"ras-related protein Rab-6","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_0942800","name":null,"product":"ras-related protein Rab-6, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"RAB6","evaluation":null}