+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-15487 | |||||||||
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タイトル | SDBC and SOD assembly, composite map | |||||||||
マップデータ | Composite map | |||||||||
試料 |
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生物種 | Deinococcus radiodurans R1 (放射線耐性) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.5 Å | |||||||||
データ登録者 | Farci D / Piano D | |||||||||
資金援助 | ポーランド, 1件
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引用 | ジャーナル: J Biol Chem / 年: 2023 タイトル: The SDBC is active in quenching oxidative conditions and bridges the cell envelope layers in Deinococcus radiodurans. 著者: Domenica Farci / André T Graça / Luca Iesu / Daniele de Sanctis / Dario Piano / 要旨: Deinococcus radiodurans is known for its remarkable ability to withstand harsh stressful conditions. The outermost layer of its cell envelope is a proteinaceous coat, the S-layer, essential for ...Deinococcus radiodurans is known for its remarkable ability to withstand harsh stressful conditions. The outermost layer of its cell envelope is a proteinaceous coat, the S-layer, essential for resistance to and interactions with the environment. The S-layer Deinoxanthin-binding complex (SDBC), one of the main units of the characteristic multilayered cell envelope of this bacterium, protects against environmental stressors and allows exchanges with the environment. So far, specific regions of this complex, the collar and the stalk, remained unassigned. Here, these regions are resolved by cryo-EM and locally refined. The resulting 3D map shows that the collar region of this multiprotein complex is a trimer of the protein DR_0644, a Cu-only superoxide dismutase (SOD) identified here to be efficient in quenching reactive oxygen species. The same data also showed that the stalk region consists of a coiled coil that extends into the cell envelope for ∼280 Å, reaching the inner membrane. Finally, the orientation and localization of the complex are defined by in situ cryo-electron crystallography. The structural organization of the SDBC couples fundamental UV antenna properties with the presence of a Cu-only SOD, showing here coexisting photoprotective and chemoprotective functions. These features suggests how the SDBC and similar protein complexes, might have played a primary role as evolutive templates for the origin of photoautotrophic processes by combining primary protective needs with more independent energetic strategies. | |||||||||
履歴 |
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-構造の表示
添付画像 |
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-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_15487.map.gz | 483.6 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-15487-v30.xml emd-15487.xml | 9.3 KB 9.3 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_15487.png | 15.6 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-15487 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15487 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_15487_validation.pdf.gz | 405.4 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_15487_full_validation.pdf.gz | 404.9 KB | 表示 | |
XML形式データ | emd_15487_validation.xml.gz | 4.4 KB | 表示 | |
CIF形式データ | emd_15487_validation.cif.gz | 5 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15487 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15487 | HTTPS FTP |
-関連構造データ
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
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-マップ
ファイル | ダウンロード / ファイル: emd_15487.map.gz / 形式: CCP4 / 大きさ: 1.1 GB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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注釈 | Composite map | ||||||||||||||||||||||||||||||||||||
投影像・断面図 | 画像のコントロール
画像は Spider により作成 これらの図は立方格子座標系で作成されたものです | ||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 0.818 Å | ||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
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-添付データ
-試料の構成要素
-全体 : SDBC and SOD assembly, composite map
全体 | 名称: SDBC and SOD assembly, composite map |
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要素 |
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-超分子 #1: SDBC and SOD assembly, composite map
超分子 | 名称: SDBC and SOD assembly, composite map / タイプ: complex / ID: 1 / キメラ: Yes / 親要素: 0 / 含まれる分子: #1 詳細: This map is a composite map of the maps with deposition codes EMD-15382 and EMD-15384, and it is the composite map for the model with deposition code PDB-8AGD. The map has to be used as a ...詳細: This map is a composite map of the maps with deposition codes EMD-15382 and EMD-15384, and it is the composite map for the model with deposition code PDB-8AGD. The map has to be used as a consensus map of the full structure (PDB-8AGD). |
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由来(天然) | 生物種: Deinococcus radiodurans R1 (放射線耐性) |
分子量 | 理論値: 800 KDa |
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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解析 | 単粒子再構成法 |
試料の集合状態 | particle |
-試料調製
緩衝液 | pH: 7.4 |
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凍結 | 凍結剤: ETHANE / 装置: FEI VITROBOT MARK IV |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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撮影 | フィルム・検出器のモデル: GATAN K2 QUANTUM (4k x 4k) 平均電子線量: 1.3 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 照射モード: SPOT SCAN / 撮影モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 1.0 µm / 最小 デフォーカス(公称値): 0.5 µm |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 3.5 Å / 解像度の算出法: FSC 0.143 CUT-OFF 詳細: This map is a composite map of the maps with deposition codes EMD-15382 and EMD-15384, and it is the composite map for the model with deposition code PDB-8AGD. This map is a composite map of ...詳細: This map is a composite map of the maps with deposition codes EMD-15382 and EMD-15384, and it is the composite map for the model with deposition code PDB-8AGD. This map is a composite map of the maps with deposition codes EMD-15382 and EMD-15384, and it is the composite map for the model with deposition code PDB-8AGD. The map has to be used as a consensus map of the full structure (PDB-8AGD). 使用した粒子像数: 252122 |
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初期 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD |