{"id":"58058b2c-f862-5df5-b99d-c4b02e621e0b","stable_key":"434e1e27-eb90-583a-956b-62472726ffba:calcium-gla-phosphatidylserine-binding","predicate":"supports_binding_of","statement":"In the bovine prothrombin Gla-domain structure, the lysophosphatidylserine headgroup contacted domain-bound Ca2+ and gamma-carboxyglutamate residues.","claim_class":"mechanistic","status":"source_derived_draft","evidence_grade":"ungraded","direction":"positive","is_public":true,"mechanism_event_id":"43830784-8d83-53dc-b89b-ffbba9ee410f","mechanism_event_label":"Protein-bound calcium helps a clotting protein recognize a membrane lipid headgroup.","subject":{"id":"e359bc15-e675-5d83-b0fe-1d70814e130b","slug":"calcium-ion","display_name":"Calcium ion","entity_type_key":"ion"},"object":{"id":"de5b9ed3-9d48-5f7e-9a9a-c734c2da1b81","slug":"prothrombin-gla-domain","display_name":"Gamma-carboxylated prothrombin Gla domain","entity_type_key":"protein_state"},"evidence_count":1,"mechanism_event":{"id":"43830784-8d83-53dc-b89b-ffbba9ee410f","stable_key":"434e1e27-eb90-583a-956b-62472726ffba:calcium-gla-phosphatidylserine-binding-event","event_type":"biochemical_relationship","label":"Protein-bound calcium helps a clotting protein recognize a membrane lipid headgroup.","description":"In the bovine prothrombin Gla-domain structure, the lysophosphatidylserine headgroup contacted domain-bound Ca2+ and gamma-carboxyglutamate residues.","status":"provisional","compartment":{"slug":"extracellular-space","display_name":"Extracellular space"},"participants":[{"entity":{"id":"e359bc15-e675-5d83-b0fe-1d70814e130b","slug":"calcium-ion","display_name":"Calcium ion","entity_type_key":"ion"},"role":"bound_coordination_cofactor","stoichiometry":null,"state_label":"","sequence_order":0,"notes":""},{"entity":{"id":"7831d47f-191c-5515-8202-534bc962e1ad","slug":"f2","display_name":"Prothrombin / coagulation factor II / F2","entity_type_key":"protein"},"role":"parent_clotting_protein","stoichiometry":null,"state_label":"","sequence_order":1,"notes":""},{"entity":{"id":"de5b9ed3-9d48-5f7e-9a9a-c734c2da1b81","slug":"prothrombin-gla-domain","display_name":"Gamma-carboxylated prothrombin Gla domain","entity_type_key":"protein_state"},"role":"carboxylated_binding_domain","stoichiometry":null,"state_label":"","sequence_order":2,"notes":""},{"entity":{"id":"4400608d-ec2d-5a58-bfe6-e382c23184c8","slug":"lysophosphatidylserine","display_name":"Lysophosphatidylserine","entity_type_key":"lipid"},"role":"directly_tested_lipid_ligand","stoichiometry":null,"state_label":"","sequence_order":3,"notes":""},{"entity":{"id":"0e2dd859-6135-556e-938f-d177f1e8c1ad","slug":"phosphatidylserine","display_name":"Phosphatidylserine","entity_type_key":"lipid"},"role":"membrane_headgroup_context","stoichiometry":null,"state_label":"","sequence_order":4,"notes":""},{"entity":{"id":"3dcbbcaa-17df-54a0-a499-9b966a38631a","slug":"extracellular-space","display_name":"Extracellular space","entity_type_key":"organelle"},"role":"experimental_location","stoichiometry":null,"state_label":"","sequence_order":5,"notes":"Study location; presence here is not a separate transport or causal claim."},{"entity":{"id":"f0b6bcb6-5d41-5d9d-af9f-6af1a94d5c5a","slug":"plasma-membrane","display_name":"Plasma membrane","entity_type_key":"organelle"},"role":"experimental_location","stoichiometry":null,"state_label":"","sequence_order":6,"notes":"Study location; presence here is not a separate transport or causal claim."}]},"contexts":[{"dimension":"compartment_description","value_text":"Extracellular protein-membrane interface","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"experimental_model","value_text":"X-ray crystallography and NMR with lysophosphatidylserine","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"limitations","value_text":"The carboxylated Gla domain is a vitamin-K-dependent protein state; calcium binding does not perform gamma-carboxylation.","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"nutrient_topic","value_text":"Calcium research collection; topical membership is not evidence of a direct dietary effect.","comparator":null,"unit":null,"notes":"","entity":{"slug":"calcium","display_name":"Calcium","entity_type_key":"nutrient_element"}},{"dimension":"organism","value_text":"Bos taurus","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"plain_language","value_text":"Protein-bound calcium helps a clotting protein recognize a membrane lipid headgroup.","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"primary_references","value_text":"[huang2003] Structural basis of membrane binding by Gla domains of vitamin K-dependent proteins (2003). https://www.nature.com/articles/nsb971 DOI: 10.1038/nsb971","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"tissue_or_cell_type","value_text":"Purified prothrombin fragment; blood-protein context","comparator":null,"unit":null,"notes":"","entity":null}],"evidence":[{"id":"8530e852-3b39-54d2-b60b-67e493d3a25f","evidence_kind":"source_excerpt","locator":"Lines 1104-1114","start_line":1104,"end_line":1114,"excerpt":"### calcium-gla-phosphatidylserine-binding\nIn the bovine prothrombin Gla-domain structure, the lysophosphatidylserine headgroup contacted domain-bound Ca2+ and gamma-carboxyglutamate residues.\nCondition category: normal\nnutrient_topic: Calcium research collection; topical membership is not evidence of a direct dietary effect.\nplain_language: Protein-bound calcium helps a clotting protein recognize a membrane lipid headgroup.\norganism: Bos taurus\ntissue_or_cell_type: Purified prothrombin fragment; blood-protein context\nexperimental_model: X-ray crystallography and NMR with lysophosphatidylserine\nlimitations: The carboxylated Gla domain is a vitamin-K-dependent protein state; calcium binding does not perform gamma-carboxylation.\ncompartment_description: Extracellular protein-membrane interface\n[huang2003] Structural basis of membrane binding by Gla domains of vitamin K-dependent proteins (2003). https://www.nature.com/articles/nsb971 DOI: 10.1038/nsb971","model_system":"X-ray crystallography and NMR with lysophosphatidylserine","directness":"author_interpretation","verification_status":"source_derived_draft","notes":"Exact curation-document quotation, not publisher quotation. Study references: [huang2003] Structural basis of membrane binding by Gla domains of vitamin K-dependent proteins (2003). https://www.nature.com/articles/nsb971 DOI: 10.1038/nsb971","relationship":"supports","weight":1.0,"link_notes":"","source":{"id":"3c083fa0-59c6-50e9-af42-678d0e3c1006","stable_key":"import-434e1e27-eb90-583a-956b-62472726ffba","title":"Calcium: mechanism-first literature curation (2026-09-17)","document_type":"imported_text","citation_label":"AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text.","file_path":"","sha256":"965c934d6b147f2b62f8d45ce6d7a87681a600bfe5c46a585b4704889afd3fc1","revision_id":"543ec48b-4f70-5197-9d76-f5a3c443664c","review_status":"unverified_draft","notes":""}}],"relations":[],"conflicts":[],"corrections":[],"research":null}