+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 6sgy | |||||||||||||||||||||
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タイトル | Structure of EccB3 dimer from the ESX-3 core complex | |||||||||||||||||||||
要素 | ESX-3 secretion system protein EccB3 | |||||||||||||||||||||
キーワード | MEMBRANE PROTEIN / Type VII Secretion System ESX-3 secretion system T7SS ESX-3 Mycobacterium smegmatis | |||||||||||||||||||||
機能・相同性 | Type VII secretion system EccB / Type VII secretion system EccB, repeat 3 domain / Type VII secretion system EccB, repeat 1 domain / Type VII secretion system ESX-1, transport TM domain B / 加水分解酵素; 酸無水物に作用 / hydrolase activity / ATP binding / plasma membrane / ESX-3 secretion system ATPase EccB3 機能・相同性情報 | |||||||||||||||||||||
生物種 | Mycobacterium smegmatis (バクテリア) | |||||||||||||||||||||
手法 | 電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 4.6 Å | |||||||||||||||||||||
データ登録者 | Famelis, N. / Rivera-Calzada, A. / Llorca, O. / Geibel, S. | |||||||||||||||||||||
資金援助 | ドイツ, スペイン, 6件
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引用 | ジャーナル: Nature / 年: 2019 タイトル: Architecture of the mycobacterial type VII secretion system. 著者: Nikolaos Famelis / Angel Rivera-Calzada / Gianluca Degliesposti / Maria Wingender / Nicole Mietrach / J Mark Skehel / Rafael Fernandez-Leiro / Bettina Böttcher / Andreas Schlosser / Oscar ...著者: Nikolaos Famelis / Angel Rivera-Calzada / Gianluca Degliesposti / Maria Wingender / Nicole Mietrach / J Mark Skehel / Rafael Fernandez-Leiro / Bettina Böttcher / Andreas Schlosser / Oscar Llorca / Sebastian Geibel / 要旨: Host infection by pathogenic mycobacteria, such as Mycobacterium tuberculosis, is facilitated by virulence factors that are secreted by type VII secretion systems. A molecular understanding of the ...Host infection by pathogenic mycobacteria, such as Mycobacterium tuberculosis, is facilitated by virulence factors that are secreted by type VII secretion systems. A molecular understanding of the type VII secretion mechanism has been hampered owing to a lack of three-dimensional structures of the fully assembled secretion apparatus. Here we report the cryo-electron microscopy structure of a membrane-embedded core complex of the ESX-3/type VII secretion system from Mycobacterium smegmatis. The core of the ESX-3 secretion machine consists of four protein components-EccB3, EccC3, EccD3 and EccE3, in a 1:1:2:1 stoichiometry-which form two identical protomers. The EccC3 coupling protein comprises a flexible array of four ATPase domains, which are linked to the membrane through a stalk domain. The domain of unknown function (DUF) adjacent to the stalk is identified as an ATPase domain that is essential for secretion. EccB3 is predominantly periplasmatic, but a small segment crosses the membrane and contacts the stalk domain. This suggests that conformational changes in the stalk domain-triggered by substrate binding at the distal end of EccC3 and subsequent ATP hydrolysis in the DUF-could be coupled to substrate secretion to the periplasm. Our results reveal that the architecture of type VII secretion systems differs markedly from that of other known secretion machines, and provide a structural understanding of these systems that will be useful for the design of antimicrobial strategies that target bacterial virulence. | |||||||||||||||||||||
履歴 |
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-構造の表示
ムービー |
ムービービューア |
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構造ビューア | 分子: MolmilJmol/JSmol |
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 6sgy.cif.gz | 134.3 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb6sgy.ent.gz | 101 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 6sgy.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
文書・要旨 | 6sgy_validation.pdf.gz | 673.1 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 6sgy_full_validation.pdf.gz | 684.8 KB | 表示 | |
XML形式データ | 6sgy_validation.xml.gz | 34.3 KB | 表示 | |
CIF形式データ | 6sgy_validation.cif.gz | 51.2 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/sg/6sgy ftp://data.pdbj.org/pub/pdb/validation_reports/sg/6sgy | HTTPS FTP |
-関連構造データ
-リンク
-集合体
登録構造単位 |
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-要素
#1: タンパク質 | 分子量: 42746.754 Da / 分子数: 2 / 由来タイプ: 組換発現 由来: (組換発現) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (バクテリア) 遺伝子: eccB3, MSMEG_0616, MSMEI_0600 発現宿主: Mycolicibacterium smegmatis MC2 155 (バクテリア) 参照: UniProt: A0QQ39 Has protein modification | Y | |
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-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
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EM実験 | 試料の集合状態: PARTICLE / 3次元再構成法: 単粒子再構成法 |
-試料調製
構成要素 | 名称: EccB3 dimeric structure from ESX-3/Type VII secretion system タイプ: COMPLEX 詳細: The sample consists of four protein components, EccB3:EccC3:EccD3:EccE3 in a 1:1:2:1 stoichiometry Molecular weight of the complex without the amphipol micelle: 0.65 MDa Entity ID: all / 由来: RECOMBINANT |
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分子量 | 値: 0.083 MDa / 実験値: NO |
由来(天然) | 生物種: Mycolicibacterium smegmatis MC2 155 (バクテリア) |
由来(組換発現) | 生物種: Mycolicibacterium smegmatis MC2 155 (バクテリア) |
緩衝液 | pH: 8 / 詳細: 30 mM Hepes pH 8.0, 150 mM NaCl |
試料 | 濃度: 0.3 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES / 詳細: bound to Amphipol A8-35 |
急速凍結 | 装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE / 湿度: 100 % / 凍結前の試料温度: 278 K / 詳細: Blotting time: 3s Blotting force: -10 |
-電子顕微鏡撮影
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TITAN KRIOS |
電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: SPOT SCAN |
電子レンズ | モード: BRIGHT FIELD / 倍率(公称値): 75000 X / 最大 デフォーカス(公称値): 2600 nm / 最小 デフォーカス(公称値): 1600 nm / Cs: 2.7 mm |
試料ホルダ | 凍結剤: NITROGEN 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER |
撮影 | 電子線照射量: 50 e/Å2 / 検出モード: COUNTING フィルム・検出器のモデル: FEI FALCON III (4k x 4k) 実像数: 11903 詳細: Images acquired as 55 frames movies at a calibrated magnification of 1.0635 Angs/px |
-解析
EMソフトウェア |
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画像処理 | 詳細: Images were collected in counting mode | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
粒子像の選択 | 選択した粒子像数: 2066007 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
対称性 | 点対称性: C2 (2回回転対称) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
3次元再構成 | 解像度: 4.6 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 55342 詳細: Particles were extracted centred at extracellular density instead than in the centre of mass in order to improve the resolution in that distal region. Extra density not corresponding to the ...詳細: Particles were extracted centred at extracellular density instead than in the centre of mass in order to improve the resolution in that distal region. Extra density not corresponding to the EccB3 dimer was subtracted 対称性のタイプ: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子モデル構築 | プロトコル: AB INITIO MODEL / 空間: REAL / Target criteria: Map correlation coefficient 詳細: Two copies of the periplasmic domain of a EccB3 homology model (based on pdb 3X3M) were fitted into the density and then morphing was performed using PHENIX Real-Space Refinement. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子モデル構築 | PDB-ID: 3X3M PDB chain-ID: A / Accession code: 3X3M / Pdb chain residue range: 100-518 / Source name: PDB / タイプ: experimental model |