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データを開く
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基本情報
登録情報 | データベース: PDB / ID: 2zle | ||||||
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タイトル | Cryo-EM structure of DegP12/OMP | ||||||
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![]() | HYDROLASE / DegP / HtrA / protease / chaperone / PDZ / outer membrane protein / OMP / periplasm / Serine protease / Stress response / Ion transport / Phage recognition / Porin / Transmembrane / Transport | ||||||
機能・相同性 | ![]() peptidase Do / programmed cell death / response to temperature stimulus / porin activity / pore complex / protein quality control for misfolded or incompletely synthesized proteins / chaperone-mediated protein folding / monoatomic ion transmembrane transport / serine-type peptidase activity / cell outer membrane ...peptidase Do / programmed cell death / response to temperature stimulus / porin activity / pore complex / protein quality control for misfolded or incompletely synthesized proteins / chaperone-mediated protein folding / monoatomic ion transmembrane transport / serine-type peptidase activity / cell outer membrane / protein folding / virus receptor activity / peptidase activity / response to heat / outer membrane-bounded periplasmic space / response to oxidative stress / periplasmic space / receptor-mediated virion attachment to host cell / positive regulation of apoptotic process / serine-type endopeptidase activity / DNA damage response / proteolysis / identical protein binding / metal ion binding / plasma membrane 類似検索 - 分子機能 | ||||||
生物種 | ![]() ![]() | ||||||
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: 28 Å | ||||||
![]() | Schaefer, E. / Saibil, H.R. | ||||||
![]() | ![]() タイトル: Structural basis for the regulated protease and chaperone function of DegP. 著者: Tobias Krojer / Justyna Sawa / Eva Schäfer / Helen R Saibil / Michael Ehrmann / Tim Clausen / ![]() 要旨: All organisms have to monitor the folding state of cellular proteins precisely. The heat-shock protein DegP is a protein quality control factor in the bacterial envelope that is involved in ...All organisms have to monitor the folding state of cellular proteins precisely. The heat-shock protein DegP is a protein quality control factor in the bacterial envelope that is involved in eliminating misfolded proteins and in the biogenesis of outer-membrane proteins. Here we describe the molecular mechanisms underlying the regulated protease and chaperone function of DegP from Escherichia coli. We show that binding of misfolded proteins transforms hexameric DegP into large, catalytically active 12-meric and 24-meric multimers. A structural analysis of these particles revealed that DegP represents a protein packaging device whose central compartment is adaptable to the size and concentration of substrate. Moreover, the inner cavity serves antagonistic functions. Whereas the encapsulation of folded protomers of outer-membrane proteins is protective and might allow safe transit through the periplasm, misfolded proteins are eliminated in the molecular reaction chamber. Oligomer reassembly and concomitant activation on substrate binding may also be critical in regulating other HtrA proteases implicated in protein-folding diseases. | ||||||
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構造の表示
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構造ビューア | 分子: ![]() ![]() |
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-検証レポート
文書・要旨 | ![]() | 891.3 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 1.5 MB | 表示 | |
XML形式データ | ![]() | 222.8 KB | 表示 | |
CIF形式データ | ![]() | 311.5 KB | 表示 | |
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-関連構造データ
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リンク
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集合体
登録構造単位 | ![]()
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要素
#1: タンパク質 | 分子量: 46868.926 Da / 分子数: 12 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() ![]() 参照: UniProt: P0C0V0, 加水分解酵素; プロテアーゼ; ペプチド結合加水分解酵素; セリンエンドペプチターゼ #2: タンパク質 | | 分子量: 38336.242 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() ![]() |
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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 |
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試料調製
構成要素 | 名称: DegP24mer with bound Omp / タイプ: COMPLEX |
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試料 | 濃度: 0.16 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
試料支持 | 詳細: C-FLAT HOLEY CARBON GRIDS |
急速凍結 | 装置: FEI VITROBOT MARK I / 凍結剤: ETHANE 詳細: Embedded in vitreous ice using C-flat holey carbon grids (CF-2/2-4C-100, Protochip) and a Vitrobot (FEI) at 20 temperature and 100% relative humidity |
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電子顕微鏡撮影
実験機器 | ![]() モデル: Tecnai F20 / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TECNAI F20 |
電子銃 | 電子線源: ![]() |
電子レンズ | モード: OTHER / 倍率(公称値): 68100 X |
画像スキャン | デジタル画像の数: 64 |
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解析
CTF補正 | 詳細: phase flipping | ||||||||||||
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対称性 | 点対称性: C1 (非対称) | ||||||||||||
3次元再構成 | 解像度: 28 Å / 粒子像の数: 6285 / ピクセルサイズ(公称値): 4.44 Å 詳細: This structure is docking of four DegP trimers (PDB ID 1KY9) and an OmpC monomer (PDB ID 2J1N) into an EM map by hand at 28A resolution. At this low resolution, no exact fitting can be done. 対称性のタイプ: POINT | ||||||||||||
精密化ステップ | サイクル: LAST
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