+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 2ob7 | ||||||
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タイトル | Structure of tmRNA-(SmpB)2 complex as inferred from cryo-EM | ||||||
要素 |
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キーワード | RNA BINDING PROTEIN/RNA / tmRNA / SmpB / RNA BINDING PROTEIN-RNA COMPLEX | ||||||
機能・相同性 | 機能・相同性情報 | ||||||
生物種 | Thermus thermophilus (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: 13.6 Å | ||||||
データ登録者 | Frank, J. / Felden, B. / Gillet, R. / Li, W. | ||||||
引用 | ジャーナル: J Biol Chem / 年: 2007 タイトル: Scaffolding as an organizing principle in trans-translation. The roles of small protein B and ribosomal protein S1. 著者: Reynald Gillet / Sukhjit Kaur / Wen Li / Marc Hallier / Brice Felden / Joachim Frank / 要旨: A eubacterial ribosome stalled on a defective mRNA can be released through a quality control mechanism referred to as trans-translation, which depends on the coordinating binding actions of transfer- ...A eubacterial ribosome stalled on a defective mRNA can be released through a quality control mechanism referred to as trans-translation, which depends on the coordinating binding actions of transfer-messenger RNA, small protein B, and ribosome protein S1. By means of cryo-electron microscopy, we obtained a map of the complex composed of a stalled ribosome and small protein B, which appears near the decoding center. This result suggests that, when lacking a codon, the A-site on the small subunit is a target for small protein B. To investigate the role of S1 played in trans-translation, we obtained a cryo-electron microscopic map, including a stalled ribosome, transfer-messenger RNA, and small protein Bs but in the absence of S1. In this complex, several connections between the 30 S subunit and transfer-messenger RNA that appear in the +S1 complex are no longer found. We propose the unifying concept of scaffolding for the roles of small protein B and S1 in binding of transfer-messenger RNA to the ribosome during trans-translation, and we infer a pathway of sequential binding events in the initial phase of trans-translation. #1: ジャーナル: Proc.Natl.Acad.Sci.USA / 年: 2006 タイトル: Cryo-EM visualization of transfer messenger RNA with two SmpBs in a stalled ribosome 著者: Kaur, S. / Gillet, R. / Li, W. / Gursky, R. / Frank, J. #2: ジャーナル: Science / 年: 2003 タイトル: Visualizing tmRNA entry into a stalled ribosome 著者: Valle, M. / Gillet, R. / Kaur, K. / Henne, A. / Ramakrishnan, V. / Frank, J. | ||||||
履歴 |
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Remark 999 | SEQUENCE The deposited entry is a model to fit the cryo-EM map of tmRNA+SmpB(2) from Thermus ...SEQUENCE The deposited entry is a model to fit the cryo-EM map of tmRNA+SmpB(2) from Thermus thermophilus. The deposition includes 4 chains: chain A: tmRNA model chains B,C: SmpB (from 1P6V.pdb chain A, for SmpB from AQUIFEX AEOLICUS); chain D: helix 44 of 30S ribosomal subunit (from 1N34.pdb chain A:1406-1496. X-ray structure of 1N34 is from Thermus thermophilus). The E.coli model eschcolitm3D-model-72.pdb (http://www.ag.auburn.edu/mirror/tmRDB/rna/tmrna.html/) was used as a template to build the model by replacing several fragments which have x-ray crystal as alternatives, and by fitting all the structures into the cryo-EM maps. Nucleotide numbering in this model follows E.coli sequence. Considering the differences between tmRNA sequences from E.coli and T.thermophilus, a small number of nucleotides in the template model are not included in this model. |
-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 | 2ob7.cif.gz | 37.5 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb2ob7.ent.gz | 18.2 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 2ob7.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 | 2ob7_validation.pdf.gz | 762.8 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 2ob7_full_validation.pdf.gz | 763.9 KB | 表示 | |
XML形式データ | 2ob7_validation.xml.gz | 14.4 KB | 表示 | |
CIF形式データ | 2ob7_validation.cif.gz | 20.4 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/ob/2ob7 ftp://data.pdbj.org/pub/pdb/validation_reports/ob/2ob7 | 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: RNA鎖 | 分子量: 105728.523 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Thermus thermophilus (バクテリア) |
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#2: RNA鎖 | 分子量: 27987.715 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: helix 44 of 30S ribosomal subunit / 由来: (天然) Thermus thermophilus (バクテリア) |
#3: タンパク質 | 分子量: 18440.818 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Thermus thermophilus (バクテリア) / 参照: UniProt: O66640*PLUS |
-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: Pre-accommodated ribosomal trans-translation complex: T. thermophilus 70S-mRNA-(P-site tRNA)-tmRNA-(SmpB)2-(EF-Tu)-GDP-kirromycin タイプ: RIBOSOME 詳細: see Experimental Procedures in Kaur et al. (PNAS). [Deposition refers to structure of tmRNA-(SmpB)2 complex derived by fitting of EM map from Kaur et al. Fitting was modified in Gillet et al.] |
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緩衝液 | 名称: polimix / pH: 7.5 / 詳細: polimix |
試料 | 濃度: 32 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: This grid plus sample was kept at -80 degree C for several days before use. |
急速凍結 | 装置: FEI VITROBOT MARK I / 凍結剤: ETHANE 詳細: Blot for 5 seconds before plunging. Rapid plunge freezing in liquid ethane. |
-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 / 日付: 2004年6月1日 |
電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 200 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELD / 倍率(公称値): 55000 X / 倍率(補正後): 49000 X / 最大 デフォーカス(公称値): 3635 nm / 最小 デフォーカス(公称値): 1475 nm / Cs: 2 mm |
試料ホルダ | 温度: 296 K / 傾斜角・最大: 0 ° / 傾斜角・最小: 0 ° |
撮影 | 電子線照射量: 15 e/Å2 / フィルム・検出器のモデル: KODAK SO-163 FILM |
-解析
EMソフトウェア |
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CTF補正 | 詳細: CTF correction of each defocus group reconstruction, by Wiener filtering | ||||||||||||
対称性 | 点対称性: C1 (非対称) | ||||||||||||
3次元再構成 | 手法: single particle reconstruction / 解像度: 13.6 Å / 粒子像の数: 52829 / ピクセルサイズ(公称値): 2.82 Å / 対称性のタイプ: POINT | ||||||||||||
原子モデル構築 | プロトコル: OTHER / 空間: REAL 詳細: METHOD--manual fitting using stereo visualization REFINEMENT PROTOCOL--Manual | ||||||||||||
原子モデル構築 | PDB-ID: 1P6V Accession code: 1P6V / 詳細: 1P6V FOR SMPB AND TLD OF TMRNA / Source name: PDB / タイプ: experimental model | ||||||||||||
精密化ステップ | サイクル: LAST
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