{
  "vercy": "1.0-draft",
  "publication": {
    "status": "research-draft",
    "adjudicationStatus": "unreviewed",
    "publishableCanonical": false,
    "generatedAt": "2026-09-13T21:11:33Z",
    "providers": [
      "Claude"
    ],
    "breadth": "written by Claude from model knowledge without web access - no source was read, every claim is a lead to verify",
    "pass": 2,
    "wave": 4,
    "engine": "claude",
    "enrichment": {
      "pass": 3,
      "engine": "claude",
      "producedAt": "2026-10-06T11:00:00Z",
      "ingestedAt": "2026-10-06T07:35:34+00:00",
      "fields": [
        "agent_conduct",
        "ethics",
        "owners"
      ]
    },
    "gate": {
      "passed": true,
      "version": "1.0",
      "at": "2026-10-06T19:51:56+00:00",
      "evidence": [
        "completeness 1.00",
        "sense: Wikidata description",
        "2 live sources",
        "review by codex: pass"
      ]
    }
  },
  "metaModel": {
    "id": "THING-Q204785",
    "registryId": "vr.tr.zinc-finger",
    "name": "zinc finger",
    "version": "0.2.0-wave.4",
    "entryKind": "thing",
    "family": "Thing Registry",
    "domain": [
      "XCT.QLT"
    ],
    "status": "research-draft"
  },
  "canonicalUrl": "https://ver.cy/models/thing/q204785/",
  "model": {
    "registry_id": "vr.tr.zinc-finger",
    "name": "zinc finger",
    "purpose": "Let an agent explain zinc fingers, relay structure, classes, functions and biotechnology uses from structural biology sources, describe the named domain types and proteins, and distinguish zinc fingers from other DNA-binding motifs, zinc as a nutrient, TALENs and CRISPR systems.",
    "definition": "A small protein structural motif in which one or more zinc ions are coordinated by cysteine and histidine residues to stabilise the fold, first identified in the transcription factor TFIIIA in 1985 through work including that of Aaron Klug, and found in many protein families, including the classical Cys2-His2 zinc fingers of DNA-binding transcription factors, RING finger domains of E3 ubiquitin ligases such as RNF4, RNF141 and RNF146, and MYND-type zinc fingers; engineered zinc finger nucleases were an early tool for targeted genome editing.",
    "what_it_is_for": "Stabilising protein folds for binding DNA, RNA, proteins and lipids.",
    "affordances": [
      "explain structure",
      "relay classes and functions",
      "describe named domains",
      "relay genome editing uses"
    ],
    "distinguishing_features": [
      "Zinc coordination",
      "Small domains",
      "Very common",
      "Engineerable binding"
    ],
    "appearance": "Not a visible object; seen in molecular models as a finger-like loop around a zinc ion.",
    "visual_identification": [
      "Zinc-stabilised protein motif",
      "Zinc finger MYND-type, RING-type zinc finger, Cys2-His2 zinc finger, RNF4, RNF146 and RNF141 RING fingers",
      "Helix-turn-helix and leucine zippers are other motifs; dietary zinc is a mineral; TALENs and CRISPR are other editing tools"
    ],
    "physical_properties": [
      {
        "quantity": "first identified",
        "typical_range": "1985",
        "unit": "year",
        "note": "TFIIIA"
      },
      {
        "quantity": "classical motif",
        "typical_range": "C2H2 with about 30 amino acids",
        "unit": "note",
        "note": ""
      },
      {
        "quantity": "human C2H2 zinc finger proteins",
        "typical_range": "over 700",
        "unit": "count",
        "note": "approximate"
      }
    ],
    "families_and_kinds": [
      "C2H2 zinc fingers",
      "RING fingers",
      "PHD fingers",
      "MYND zinc fingers",
      "treble clef and zinc ribbon folds",
      "zinc finger nucleases"
    ],
    "related_models": [
      {
        "relation": "is a kind of",
        "target": "amino acid motifs",
        "why": "in registry terms"
      },
      {
        "relation": "binds",
        "target": "zinc",
        "why": ""
      },
      {
        "relation": "includes",
        "target": "RING finger domain",
        "why": ""
      },
      {
        "relation": "is used in",
        "target": "zinc finger nuclease",
        "why": ""
      }
    ],
    "identifiers": [],
    "standards_and_regulation": [
      "InterPro and Pfam domain classifications",
      "Gene therapy regulation for zinc finger nuclease therapies"
    ],
    "failure_modes_and_hazards": [
      "Treating named proteins as motif classes",
      "Confusing zinc fingers with dietary zinc",
      "Overstating editing precision"
    ],
    "in_scope": [],
    "out_of_scope": [],
    "characteristics": [],
    "agent_conduct": {
      "may": [
        "Explain zinc finger structure and its role in DNA and protein binding from molecular biology sources.",
        "Annotate zinc finger motifs in sequences it is authorized to analyse."
      ],
      "must_not": [
        "Present zinc finger gene-editing research as ready treatment for patients.",
        "Assist in editing human germline cells outside lawful, ethically approved research.",
        "Fabricate or misreport binding data."
      ],
      "requires_human": [
        "Using zinc finger based editing results in clinical or heritable applications."
      ]
    },
    "ethics": {
      "considerations": [
        "Engineered zinc fingers are gene-editing tools; heritable edits raise lasting ethical questions."
      ],
      "affected_parties": [
        "Patients in trials",
        "Future generations",
        "Researchers"
      ]
    },
    "owners": {
      "steward": "Nobody owns the motif; patent holders own specific engineered tools.",
      "master_systems": []
    }
  },
  "sources": [
    {
      "id": "wikidata",
      "title": "Wikidata item Q204785: zinc finger",
      "url": "https://www.wikidata.org/wiki/Q204785",
      "url_status": "live",
      "what_it_supports": "identity and sense of the item",
      "checked_by": "wikidata-api"
    },
    {
      "id": "wikipedia-en",
      "title": "Wikipedia: Zinc finger",
      "url": "https://en.wikipedia.org/wiki/Zinc_finger",
      "url_status": "live",
      "what_it_supports": "general description of the item",
      "checked_by": "wikidata-api sitelink"
    }
  ],
  "structure": {
    "bundles": [
      {
        "id": "understand",
        "name": "Understand",
        "description": "What a zinc finger is.",
        "rationale": "Science.",
        "layers": [
          {
            "id": "definition",
            "name": "Definition",
            "description": "Definition.",
            "findings": [
              {
                "id": "definition-finding",
                "name": "Definition",
                "description": "Definition.",
                "questions": [
                  {
                    "text": "What is a zinc finger, and how does it differ from other DNA-binding motifs, dietary zinc, TALENs and CRISPR?",
                    "kind": "definition"
                  },
                  {
                    "text": "Is the question about structure, a specific protein or genome editing?",
                    "kind": "boundary"
                  }
                ]
              }
            ]
          },
          {
            "id": "named",
            "name": "Named",
            "description": "Named domains.",
            "findings": [
              {
                "id": "named-finding",
                "name": "Named",
                "description": "Named.",
                "questions": [
                  {
                    "text": "What are MYND-type, RING-type and Cys2-His2 zinc fingers and the RNF4, RNF141 and RNF146 RING fingers?",
                    "kind": "definition"
                  },
                  {
                    "text": "Which entry fits the specific domain?",
                    "kind": "action"
                  }
                ]
              }
            ]
          }
        ]
      },
      {
        "id": "structure",
        "name": "Structure",
        "description": "Structure.",
        "rationale": "Science.",
        "layers": [
          {
            "id": "fold",
            "name": "Fold",
            "description": "Fold and coordination.",
            "findings": [
              {
                "id": "fold-finding",
                "name": "Fold",
                "description": "Fold.",
                "questions": [
                  {
                    "text": "How do cysteine and histidine residues coordinate zinc?",
                    "kind": "provenance"
                  },
                  {
                    "text": "Which references are standard?",
                    "kind": "provenance"
                  }
                ]
              }
            ]
          },
          {
            "id": "dna",
            "name": "DNA binding",
            "description": "DNA recognition.",
            "findings": [
              {
                "id": "dna-finding",
                "name": "DNA binding",
                "description": "DNA binding.",
                "questions": [
                  {
                    "text": "How do C2H2 zinc fingers recognise DNA sequences?",
                    "kind": "provenance"
                  },
                  {
                    "text": "Which sources are cited?",
                    "kind": "provenance"
                  }
                ]
              }
            ]
          }
        ]
      },
      {
        "id": "function",
        "name": "Function",
        "description": "Functions.",
        "rationale": "Application.",
        "layers": [
          {
            "id": "ubiquitin",
            "name": "Ubiquitin",
            "description": "RING E3 ligases.",
            "findings": [
              {
                "id": "ubiquitin-finding",
                "name": "Ubiquitin",
                "description": "Ubiquitin.",
                "questions": [
                  {
                    "text": "How do RING finger proteins act as E3 ubiquitin ligases?",
                    "kind": "provenance"
                  },
                  {
                    "text": "Which entry fits ubiquitin ligase?",
                    "kind": "action"
                  }
                ]
              }
            ]
          },
          {
            "id": "editing",
            "name": "Editing",
            "description": "Genome editing.",
            "findings": [
              {
                "id": "editing-finding",
                "name": "Editing",
                "description": "Editing.",
                "questions": [
                  {
                    "text": "How were zinc finger nucleases used for genome editing, and how do they compare with CRISPR?",
                    "kind": "provenance"
                  },
                  {
                    "text": "Which entry fits zinc finger nuclease?",
                    "kind": "action"
                  }
                ]
              }
            ]
          }
        ]
      },
      {
        "id": "context",
        "name": "Context",
        "description": "History and databases.",
        "rationale": "Context.",
        "layers": [
          {
            "id": "history",
            "name": "History",
            "description": "Discovery.",
            "findings": [
              {
                "id": "history-finding",
                "name": "History",
                "description": "History.",
                "questions": [
                  {
                    "text": "How was the zinc finger discovered in TFIIIA?",
                    "kind": "provenance"
                  },
                  {
                    "text": "Which entry fits Aaron Klug?",
                    "kind": "action"
                  }
                ]
              }
            ]
          },
          {
            "id": "databases",
            "name": "Databases",
            "description": "Domain databases.",
            "findings": [
              {
                "id": "databases-finding",
                "name": "Databases",
                "description": "Databases.",
                "questions": [
                  {
                    "text": "How do InterPro and Pfam classify zinc finger domains?",
                    "kind": "provenance"
                  },
                  {
                    "text": "Which entry fits InterPro?",
                    "kind": "action"
                  }
                ]
              }
            ]
          }
        ]
      }
    ]
  },
  "openQuestions": [
    "Should RING finger proteins be split off as protein entries?",
    "How should InterPro be linked?",
    "Should zinc finger nucleases be a separate entry?"
  ],
  "statistics": {
    "bundles": 4,
    "layers": 8,
    "findings": 8,
    "questions": 16
  }
}