+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-28827 | ||||||||||||||||||||||||||||||
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タイトル | Human CCC complex | ||||||||||||||||||||||||||||||
マップデータ | Post-processed sharpened map. B factor -24 | ||||||||||||||||||||||||||||||
試料 |
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キーワード | endosomal sorting / commander / CCC complex / ENDOCYTOSIS | ||||||||||||||||||||||||||||||
機能・相同性 | 機能・相同性情報 negative regulation of sodium ion transmembrane transport / cytoplasmic sequestering of NF-kappaB / plasma membrane to endosome transport / regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of protein localization to cell surface / copper ion homeostasis / Golgi to plasma membrane transport / phosphatidic acid binding / sodium channel inhibitor activity / positive regulation of ubiquitin-dependent protein catabolic process ...negative regulation of sodium ion transmembrane transport / cytoplasmic sequestering of NF-kappaB / plasma membrane to endosome transport / regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of protein localization to cell surface / copper ion homeostasis / Golgi to plasma membrane transport / phosphatidic acid binding / sodium channel inhibitor activity / positive regulation of ubiquitin-dependent protein catabolic process / endocytic recycling / phosphatidylinositol-3,4-bisphosphate binding / phosphatidylinositol-3,5-bisphosphate binding / Cul2-RING ubiquitin ligase complex / negative regulation of NF-kappaB transcription factor activity / sodium ion transport / phosphatidylinositol-3,4,5-trisphosphate binding / cullin family protein binding / NF-kappaB binding / intracellular copper ion homeostasis / negative regulation of canonical NF-kappaB signal transduction / phosphatidylinositol-4,5-bisphosphate binding / tumor necrosis factor-mediated signaling pathway / cholesterol homeostasis / positive regulation of protein ubiquitination / nucleotide-excision repair / recycling endosome / protein transport / Neddylation / cytoplasmic vesicle / secretory granule lumen / positive regulation of canonical NF-kappaB signal transduction / ficolin-1-rich granule lumen / early endosome / endosome membrane / endosome / copper ion binding / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / centrosome / Neutrophil degranulation / Golgi apparatus / protein homodimerization activity / extracellular region / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm 類似検索 - 分子機能 | ||||||||||||||||||||||||||||||
生物種 | Homo sapiens (ヒト) | ||||||||||||||||||||||||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.53 Å | ||||||||||||||||||||||||||||||
データ登録者 | Healy MD / McNally KE / Butkovic R / Chilton M / Kato K / Sacharz J / McConville C / Moody ERR / Shaw S / Planelles-Herrero VJ ...Healy MD / McNally KE / Butkovic R / Chilton M / Kato K / Sacharz J / McConville C / Moody ERR / Shaw S / Planelles-Herrero VJ / Kadapalakere SY / Ross J / Borucu U / Palmer CS / Chen K / Croll TI / Hall RJ / Caruana NJ / Ghai R / Nguyen THD / Heesom KJ / Saitoh S / Berger I / Berger-Schaffitzel C / Williams TA / Stroud DA / Derivery E / Collins BM / Cullen PJ | ||||||||||||||||||||||||||||||
資金援助 | 英国, オーストラリア, 9件
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引用 | ジャーナル: Cell / 年: 2023 タイトル: Structure of the endosomal Commander complex linked to Ritscher-Schinzel syndrome. 著者: Michael D Healy / Kerrie E McNally / Rebeka Butkovič / Molly Chilton / Kohji Kato / Joanna Sacharz / Calum McConville / Edmund R R Moody / Shrestha Shaw / Vicente J Planelles-Herrero / ...著者: Michael D Healy / Kerrie E McNally / Rebeka Butkovič / Molly Chilton / Kohji Kato / Joanna Sacharz / Calum McConville / Edmund R R Moody / Shrestha Shaw / Vicente J Planelles-Herrero / Sathish K N Yadav / Jennifer Ross / Ufuk Borucu / Catherine S Palmer / Kai-En Chen / Tristan I Croll / Ryan J Hall / Nikeisha J Caruana / Rajesh Ghai / Thi H D Nguyen / Kate J Heesom / Shinji Saitoh / Imre Berger / Christiane Schaffitzel / Tom A Williams / David A Stroud / Emmanuel Derivery / Brett M Collins / Peter J Cullen / 要旨: The Commander complex is required for endosomal recycling of diverse transmembrane cargos and is mutated in Ritscher-Schinzel syndrome. It comprises two sub-assemblies: Retriever composed of VPS35L, ...The Commander complex is required for endosomal recycling of diverse transmembrane cargos and is mutated in Ritscher-Schinzel syndrome. It comprises two sub-assemblies: Retriever composed of VPS35L, VPS26C, and VPS29; and the CCC complex which contains twelve subunits: COMMD1-COMMD10 and the coiled-coil domain-containing (CCDC) proteins CCDC22 and CCDC93. Combining X-ray crystallography, electron cryomicroscopy, and in silico predictions, we have assembled a complete structural model of Commander. Retriever is distantly related to the endosomal Retromer complex but has unique features preventing the shared VPS29 subunit from interacting with Retromer-associated factors. The COMMD proteins form a distinctive hetero-decameric ring stabilized by extensive interactions with CCDC22 and CCDC93. These adopt a coiled-coil structure that connects the CCC and Retriever assemblies and recruits a 16th subunit, DENND10, to form the complete Commander complex. The structure allows mapping of disease-causing mutations and reveals the molecular features required for the function of this evolutionarily conserved trafficking machinery. | ||||||||||||||||||||||||||||||
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_28827.map.gz | 64.8 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-28827-v30.xml emd-28827.xml | 35.4 KB 35.4 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_28827_fsc.xml | 9.4 KB | 表示 | FSCデータファイル |
画像 | emd_28827.png | 53.3 KB | ||
Filedesc metadata | emd-28827.cif.gz | 8.7 KB | ||
その他 | emd_28827_additional_1.map.gz emd_28827_half_map_1.map.gz emd_28827_half_map_2.map.gz | 54.7 MB 54.9 MB 54.9 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-28827 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28827 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_28827_validation.pdf.gz | 1.2 MB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_28827_full_validation.pdf.gz | 1.2 MB | 表示 | |
XML形式データ | emd_28827_validation.xml.gz | 16.3 KB | 表示 | |
CIF形式データ | emd_28827_validation.cif.gz | 21.3 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28827 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28827 | 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_28827.map.gz / 形式: CCP4 / 大きさ: 70.2 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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注釈 | Post-processed sharpened map. B factor -24 | ||||||||||||||||||||||||||||||||||||
投影像・断面図 | 画像のコントロール
画像は Spider により作成 | ||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.084 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
-追加マップ: Refine 3D map
ファイル | emd_28827_additional_1.map | ||||||||||||
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注釈 | Refine 3D map | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Half map
ファイル | emd_28827_half_map_1.map | ||||||||||||
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注釈 | Half map | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Half map
ファイル | emd_28827_half_map_2.map | ||||||||||||
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注釈 | Half map | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-試料の構成要素
+全体 : Human CCC complex
+超分子 #1: Human CCC complex
+分子 #1: COMM domain-containing protein 1
+分子 #2: COMM domain-containing protein 2
+分子 #3: COMM domain-containing protein 3
+分子 #4: COMM domain-containing protein 4
+分子 #5: COMM domain-containing protein 5
+分子 #6: COMM domain-containing protein 6
+分子 #7: COMM domain-containing protein 7
+分子 #8: COMM domain-containing protein 8
+分子 #9: COMM domain-containing protein 9
+分子 #10: COMM domain-containing protein 10
+分子 #11: Coiled-coil domain-containing protein 93
+分子 #12: Coiled-coil domain-containing protein 22
-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
濃度 | 0.2 mg/mL |
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緩衝液 | pH: 7.2 詳細: 50 mM HEPES pH7.2, 150 mM NaCl, 2mM beta-mercaptoethanol, 0.01% Triton-X100 |
グリッド | モデル: Quantifoil R1.2/1.3 / 材質: COPPER / メッシュ: 300 / 支持フィルム - 材質: GRAPHENE OXIDE |
凍結 | 凍結剤: ETHANE / 装置: FEI VITROBOT MARK IV |
詳細 | Human CCC complex cross-linked with 1 mM BS3 |
-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: FEI FALCON IV (4k x 4k) 撮影したグリッド数: 2 / 実像数: 5651 / 平均露光時間: 9.01 sec. / 平均電子線量: 43.14 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: FLOOD BEAM / 撮影モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 2.0 µm / 最小 デフォーカス(公称値): 1.2 µm |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |