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基本情報
登録情報 | データベース: PDB / ID: 6j45 | |||||||||
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タイトル | Crystal structure of E. coli peptide deformylase enzyme and chaperone trigger factor fitted into the cryo-EM density map of the complex | |||||||||
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![]() | RIBOSOME / E. coli 70S ribosome / Protein biogenesis / Chaperone / Peptide deformylase / Trigger factor / Polypeptide exit tunnel / PPIase | |||||||||
機能・相同性 | ![]() peptide deformylase / peptide deformylase activity / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein transport / protein folding / translation / cell cycle / cell division / metal ion binding / cytoplasm 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: 12.2 Å | |||||||||
![]() | Sengupta, J. / Bhakta, S. / Akbar, S. | |||||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Cryo-EM Structures Reveal Relocalization of MetAP in the Presence of Other Protein Biogenesis Factors at the Ribosomal Tunnel Exit. 著者: Sayan Bhakta / Shirin Akbar / Jayati Sengupta / ![]() 要旨: During protein biosynthesis in bacteria, one of the earliest events that a nascent polypeptide chain goes through is the co-translational enzymatic processing. The event includes two enzymatic ...During protein biosynthesis in bacteria, one of the earliest events that a nascent polypeptide chain goes through is the co-translational enzymatic processing. The event includes two enzymatic pathways: deformylation of the N-terminal methionine by the enzyme peptide deformylase (PDF), followed by methionine excision catalyzed by methionine aminopeptidase (MetAP). During the enzymatic processing, the emerging nascent protein likely remains shielded by the ribosome-associated chaperone trigger factor. The ribosome tunnel exit serves as a stage for recruiting proteins involved in maturation processes of the nascent chain. Co-translational processing of nascent chains is a critical step for subsequent folding and functioning of mature proteins. Here, we present cryo-electron microscopy structures of Escherichia coli (E. coli) ribosome in complex with the nascent chain processing proteins. The structures reveal overlapping binding sites for PDF and MetAP when they bind individually at the tunnel exit site, where L22-L32 protein region provides primary anchoring sites for both proteins. In the absence of PDF, trigger factor can access ribosomal tunnel exit when MetAP occupies its primary binding site. Interestingly, however, in the presence of PDF, when MetAP's primary binding site is already engaged, MetAP has a remarkable ability to occupy an alternative binding site adjacent to PDF. Our study, thus, discloses an unexpected mechanism that MetAP adopts for context-specific ribosome association. | |||||||||
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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 | ![]() | 760.3 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 759.9 KB | 表示 | |
XML形式データ | ![]() | 18.7 KB | 表示 | |
CIF形式データ | ![]() | 26.7 KB | 表示 | |
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-関連構造データ
関連構造データ | ![]() 9778MC ![]() 9750C ![]() 9752C ![]() 9753C ![]() 9759C ![]() 6iy7C ![]() 6iz7C ![]() 6iziC ![]() 6j0aC C: 同じ文献を引用 ( M: このデータのモデリングに利用したマップデータ |
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類似構造データ |
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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: 19357.447 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() ![]() |
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#2: タンパク質 | 分子量: 48255.570 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() ![]() |
-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: E. coli 70S ribosome in complex with enzyme peptide deformylase and chaperone trigger factor タイプ: RIBOSOME 詳細: The complex was prepared by incubating E. coli 70S ribosome with peptide deformylase, methionine aminopeptidase and trigger factor in that sequence. However, cryo EM reconstruction of the ...詳細: The complex was prepared by incubating E. coli 70S ribosome with peptide deformylase, methionine aminopeptidase and trigger factor in that sequence. However, cryo EM reconstruction of the complex showed no density corresponding to methionine aminopeptidase near the ribosomal tunnel exit. Entity ID: all / 由来: MULTIPLE SOURCES | ||||||||||||
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由来(天然) |
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由来(組換発現) |
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緩衝液 | pH: 7.4 | ||||||||||||
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES | ||||||||||||
試料支持 | グリッドの材料: COPPER / グリッドのサイズ: 300 divisions/in. / グリッドのタイプ: Quantifoil R2/2 | ||||||||||||
急速凍結 | 装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE |
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電子顕微鏡撮影
実験機器 | ![]() モデル: Tecnai Polara / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI POLARA 300 |
電子銃 | 電子線源: ![]() |
電子レンズ | モード: BRIGHT FIELD |
試料ホルダ | 凍結剤: NITROGEN |
撮影 | 電子線照射量: 10 e/Å2 / フィルム・検出器のモデル: FEI EAGLE (4k x 4k) |
画像スキャン | 横: 4096 / 縦: 4096 |
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解析
EMソフトウェア | 名称: SPIDER / カテゴリ: 3次元再構成 | ||||||||||||
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CTF補正 | タイプ: PHASE FLIPPING ONLY | ||||||||||||
3次元再構成 | 解像度: 12.2 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 20900 / 対称性のタイプ: POINT | ||||||||||||
原子モデル構築 | 3D fitting-ID: 1 / PDB chain-ID: A / Source name: PDB / タイプ: experimental model
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