{
  "id": "ISB-D-0004",
  "portal_index": 4,
  "title": "MecA/ClpC/ClpP AAA⁺ protease",
  "portal_description": "Central AAA⁺ protease MecA/ClpC/ClpP from S. aureus; near-atomic cryo-EM structure, integrated with AF modelling and functional assays.",
  "portal_landing_page_url": "https://wpotrzebowski.github.io/isb_datasets/datasets/dataset-4.html",
  "unit_facility": "Cryo-EM Swedish Nat. Facility (Stockholm)",
  "system_target": "Central AAA⁺ protease MecA/ClpC/ClpP from S. aureus; near-atomic cryo-EM structure, integrated with AF modelling and functional assays.",
  "organism_source": "Staphylococcus aureus",
  "approx_data_collection_years": "~2022–2025",
  "access": {
    "status": "public",
    "license": null,
    "license_url": null
  },
  "main_public_repository_storage": "PDB + EMDB + EMPIAR + publication supplementary data + Figshare / preprint assets + SciLifeLab Data Repository",
  "techniques": [
    {
      "code": "cryo_em",
      "label": "Cryo-EM"
    },
    {
      "code": "ms_proteomics",
      "label": "MS / Proteomics"
    },
    {
      "code": "biophysics",
      "label": "Biophysics (ITC/SPR/MST/DSF etc.)"
    },
    {
      "code": "integrative_modelling",
      "label": "Integrative / computational modelling (non-MD)"
    }
  ],
  "repository_records": [
    {
      "group": "core_same_study",
      "kind": "PDB",
      "accession": "9GI1",
      "url": "https://www.rcsb.org/structure/9GI1",
      "relation": "primary_structure",
      "note": "ClpC/ClpP body; paired map EMD-51367"
    },
    {
      "group": "core_same_study",
      "kind": "PDB",
      "accession": "9GOQ",
      "url": "https://www.rcsb.org/structure/9GOQ",
      "relation": "primary_structure",
      "note": "MecA crown; paired map EMD-51498"
    },
    {
      "group": "core_same_study",
      "kind": "PDB",
      "accession": "9R2S",
      "url": "https://www.rcsb.org/structure/9R2S",
      "relation": "primary_structure",
      "note": "ClpP body; paired map EMD-53538"
    },
    {
      "group": "core_same_study",
      "kind": "PDB",
      "accession": "9RAI",
      "url": "https://www.rcsb.org/structure/9RAI",
      "relation": "primary_structure",
      "note": "Composite whole complex; paired map EMD-53879"
    },
    {
      "group": "core_same_study",
      "kind": "EMDB",
      "accession": "EMD-51367",
      "url": "https://www.ebi.ac.uk/emdb/EMD-51367",
      "relation": "primary_map",
      "note": "ClpC/ClpP body; paired model 9GI1"
    },
    {
      "group": "core_same_study",
      "kind": "EMDB",
      "accession": "EMD-51498",
      "url": "https://www.ebi.ac.uk/emdb/EMD-51498",
      "relation": "primary_map",
      "note": "MecA crown; paired model 9GOQ"
    },
    {
      "group": "core_same_study",
      "kind": "EMDB",
      "accession": "EMD-53538",
      "url": "https://www.ebi.ac.uk/emdb/EMD-53538",
      "relation": "primary_map",
      "note": "ClpP body; paired model 9R2S"
    },
    {
      "group": "core_same_study",
      "kind": "EMDB",
      "accession": "EMD-53879",
      "url": "https://www.ebi.ac.uk/emdb/EMD-53879",
      "relation": "primary_map",
      "note": "Composite whole complex; paired model 9RAI"
    },
    {
      "group": "core_same_study",
      "kind": "EMPIAR",
      "accession": "EMPIAR-12887",
      "url": "https://www.ebi.ac.uk/empiar/EMPIAR-12887",
      "relation": "raw_data",
      "note": "aligned micrographs and raw movie frames"
    },
    {
      "group": "same_study_supplementary",
      "kind": "journal_supplementary_file",
      "accession": "Supplementary Data 1",
      "url": "https://static-content.springer.com/esm/art%3A10.1038%2Fs42003-025-08908-w/MediaObjects/42003_2025_8908_MOESM4_ESM.xlsx",
      "relation": "supplementary_dataset",
      "note": "Source data for figures (XLSX); Communications Biology article."
    },
    {
      "group": "same_study_supplementary",
      "kind": "journal_supplementary_file",
      "accession": "Supplementary Video 1",
      "url": "https://static-content.springer.com/esm/art%3A10.1038%2Fs42003-025-08908-w/MediaObjects/42003_2025_8908_MOESM5_ESM.mp4",
      "relation": "supplementary_media",
      "note": "3D variability movie (MecA crown, ClpC/ClpP and ClpP bodies)."
    },
    {
      "group": "same_study_supplementary",
      "kind": "journal_supplementary_file",
      "accession": null,
      "url": "https://www.nature.com/articles/s42003-025-08908-w#MOESM2",
      "relation": "supplementary_information",
      "note": "Supplementary Information PDF (figures, tables, extended methods)."
    },
    {
      "group": "derived_computational",
      "kind": "preprint",
      "doi": "10.1101/2025.06.06.658286",
      "url": "https://doi.org/10.1101/2025.06.06.658286",
      "relation": "derived_dataset",
      "note": "AlphaFold predictions and ChimeraX session (MecA–ClpC AF models) linked from the primary publication."
    },
    {
      "group": "derived_computational",
      "kind": "SciLifeLab Data Repository",
      "accession": "29261882",
      "url": "https://figshare.scilifelab.se/articles/dataset/Structure_of_the_central_Staphylococcus_aureus_AAA_protease_MecA_ClpC_ClpP/29261882",
      "relation": "supplementary_dataset",
      "note": "SciLifeLab Figshare dataset (ChimeraX session and related assets for this publication)."
    },
    {
      "group": "derived_computational",
      "kind": "SciLifeLab Publication",
      "accession": null,
      "url": "https://publications.scilifelab.se/publication/73fee7c76bfd49a6944ca090feb04ef1",
      "relation": "institutional_record",
      "note": "SciLifeLab publications catalogue entry."
    },
    {
      "group": "related_reference_method",
      "kind": "PDB-IHM",
      "accession": "9A66",
      "url": "https://pdb-ihm.org/entry.html?9A66",
      "relation": "related_structure",
      "note": "Bacillus subtilis integrative ClpC–ClpP model (XL-MS + deep learning); not the S. aureus MecA/ClpC/ClpP cryo-EM study."
    },
    {
      "group": "related_reference_method",
      "kind": "PRIDE",
      "accession": "PXD035508",
      "url": "https://www.ebi.ac.uk/pride/archive/projects/PXD035508",
      "relation": "related_dataset",
      "note": "Crosslinking-MS data for PDB-IHM 9A66; adjacent reference, not the same experimental dataset as this portal record."
    },
    {
      "group": "related_companion_structures",
      "kind": "PDB",
      "accession": "9QCL",
      "url": "https://www.rcsb.org/structure/9QCL",
      "relation": "related_structure",
      "note": "S. aureus ClpC/ClpP (EMBO J. 2025); paired map EMD-53014"
    },
    {
      "group": "related_companion_structures",
      "kind": "PDB",
      "accession": "9QRW",
      "url": "https://www.rcsb.org/structure/9QRW",
      "relation": "related_structure",
      "note": "S. aureus ClpC/ClpP (EMBO J. 2025); paired map EMD-53324"
    },
    {
      "group": "related_companion_structures",
      "kind": "PDB",
      "accession": "9QQR",
      "url": "https://www.rcsb.org/structure/9QQR",
      "relation": "related_structure",
      "note": "S. aureus ClpC/ClpP (EMBO J. 2025); paired map EMD-53312"
    },
    {
      "group": "related_companion_structures",
      "kind": "EMDB",
      "accession": "EMD-53014",
      "url": "https://www.ebi.ac.uk/emdb/EMD-53014",
      "relation": "related_map",
      "note": "The EMBO Journal (2025) ClpC/ClpP study; paired model 9QCL"
    },
    {
      "group": "related_companion_structures",
      "kind": "EMDB",
      "accession": "EMD-53324",
      "url": "https://www.ebi.ac.uk/emdb/EMD-53324",
      "relation": "related_map",
      "note": "The EMBO Journal (2025) ClpC/ClpP study; paired model 9QRW"
    },
    {
      "group": "related_companion_structures",
      "kind": "EMDB",
      "accession": "EMD-53312",
      "url": "https://www.ebi.ac.uk/emdb/EMD-53312",
      "relation": "related_map",
      "note": "The EMBO Journal (2025) ClpC/ClpP study; paired model 9QQR"
    }
  ],
  "publications": [
    {
      "type": "journal_article",
      "title": "Structure of the central Staphylococcus aureus AAA+ protease MecA/ClpC/ClpP",
      "venue": "Communications Biology (2025)",
      "doi": "10.1038/s42003-025-08908-w",
      "url": "https://doi.org/10.1038/s42003-025-08908-w",
      "relation": "primary_publication"
    },
    {
      "type": "journal_article",
      "title": "Allosteric control of the bacterial ClpC/ClpP protease and its hijacking by antibacterial peptides",
      "venue": "The EMBO Journal (2025)",
      "doi": "10.1038/s44318-025-00575-1",
      "url": "https://doi.org/10.1038/s44318-025-00575-1",
      "relation": "related_publication",
      "note": "Resting-state and related S. aureus ClpC/ClpP cryo-EM; distinct from the MecA/ClpC/ClpP complex featured in the primary publication."
    }
  ],
  "keywords": [
    "MecA",
    "ClpC",
    "ClpP",
    "AAA+ protease",
    "Staphylococcus aureus",
    "cryo-EM"
  ]
}