+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-8328 | |||||||||
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タイトル | Pelagibacter cell with pili | |||||||||
マップデータ | A Pelagibacter cell with pili | |||||||||
試料 |
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生物種 | Candidatus pelagibacter (バクテリア) | |||||||||
手法 | 電子線トモグラフィー法 / クライオ電子顕微鏡法 | |||||||||
データ登録者 | Zhao XW / Nicastro D | |||||||||
引用 | ジャーナル: Appl Environ Microbiol / 年: 2017 タイトル: Three-Dimensional Structure of the Ultraoligotrophic Marine Bacterium "Candidatus Pelagibacter ubique". 著者: Xiaowei Zhao / Cindi L Schwartz / Jason Pierson / Stephen J Giovannoni / J Richard McIntosh / Daniela Nicastro / 要旨: SAR11 bacteria are small, heterotrophic, marine alphaproteobacteria found throughout the oceans. They thrive at the low nutrient concentrations typical of open ocean conditions, although the ...SAR11 bacteria are small, heterotrophic, marine alphaproteobacteria found throughout the oceans. They thrive at the low nutrient concentrations typical of open ocean conditions, although the adaptations required for life under those conditions are not well understood. To illuminate this issue, we used cryo-electron tomography to study "Candidatus Pelagibacter ubique" strain HTCC1062, a member of the SAR11 clade. Our results revealed its cellular dimensions and details of its intracellular organization. Frozen-hydrated cells, which were preserved in a life-like state, had an average cell volume (enclosed by the outer membrane) of 0.037 ± 0.011 μm Strikingly, the periplasmic space occupied ∼20% to 50% of the total cell volume in log-phase cells and ∼50% to 70% in stationary-phase cells. The nucleoid occupied the convex side of the crescent-shaped cells and the ribosomes predominantly occupied the concave side, at a relatively high concentration of 10,000 to 12,000 ribosomes/μm Outer membrane pore complexes, likely composed of PilQ, were frequently observed in both log-phase and stationary-phase cells. Long filaments, most likely type IV pili, were found on dividing cells. The physical dimensions, intracellular organization, and morphological changes throughout the life cycle of "Ca. Pelagibacter ubique" provide structural insights into the functional adaptions of these oligotrophic ultramicrobacteria to their habitat. IMPORTANCE: Bacterioplankton of the SAR11 clade (Pelagibacterales) are of interest because of their global biogeochemical significance and because they appear to have been molded by unusual ...IMPORTANCE: Bacterioplankton of the SAR11 clade (Pelagibacterales) are of interest because of their global biogeochemical significance and because they appear to have been molded by unusual evolutionary circumstances that favor simplicity and efficiency. They have adapted to an ecosystem in which nutrient concentrations are near the extreme limits at which transport systems can function adequately, and they have evolved streamlined genomes to execute only functions essential for life. However, little is known about the actual size limitations and cellular features of living oligotrophic ultramicrobacteria. In this study, we have used cryo-electron tomography to obtain accurate physical information about the cellular architecture of "Candidatus Pelagibacter ubique," the first cultivated member of the SAR11 clade. These results provide foundational information for answering questions about the cell architecture and functions of these ultrasmall oligotrophic bacteria. | |||||||||
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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添付画像 |
-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_8328.map.gz | 1.2 GB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-8328-v30.xml emd-8328.xml | 7.8 KB 7.8 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_8328.png | 156.3 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-8328 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8328 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_8328_validation.pdf.gz | 77.6 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_8328_full_validation.pdf.gz | 76.7 KB | 表示 | |
XML形式データ | emd_8328_validation.xml.gz | 499 B | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8328 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8328 | 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_8328.map.gz / 形式: CCP4 / 大きさ: 1.4 GB / タイプ: IMAGE STORED AS SIGNED BYTE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | A Pelagibacter cell with pili | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 9.46 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
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-添付データ
-試料の構成要素
-全体 : Pelagibacter cell with pili
全体 | 名称: Pelagibacter cell with pili |
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要素 |
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-超分子 #1: Pelagibacter cell with pili
超分子 | 名称: Pelagibacter cell with pili / タイプ: cell / ID: 1 / 親要素: 0 |
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由来(天然) | 生物種: Candidatus pelagibacter (バクテリア) |
-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 | 電子線トモグラフィー法 |
試料の集合状態 | cell |
-試料調製
緩衝液 | pH: 7 |
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グリッド | モデル: Quantifoil R2/2 / 材質: COPPER / メッシュ: 200 / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: HOLEY / 前処理 - タイプ: GLOW DISCHARGE |
凍結 | 凍結剤: ETHANE |
切片作成 | その他: NO SECTIONING |
位置合わせマーカー | Manufacturer: Sigma-Aldrich / 直径: 10 nm |
-電子顕微鏡法
顕微鏡 | FEI TECNAI F30 |
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撮影 | フィルム・検出器のモデル: GATAN ORIUS SC200 (2k x 2k) 平均電子線量: 100.0 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: OTHER / 撮影モード: BRIGHT FIELD |
実験機器 | モデル: Tecnai F30 / 画像提供: FEI Company |
-画像解析
最終 再構成 | アルゴリズム: BACK PROJECTION / ソフトウェア - 名称: IMOD (ver. 4.8.38) / 使用した粒子像数: 121 |
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