+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-1858 | |||||||||
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タイトル | Structure of the ribosome-SecYE complex in the membrane environment | |||||||||
マップデータ | This map represents an E.coli 70S ribosome carrying an elongation arrested nascent chain of 118 amino acid residues, with the first 102 residues representing the N-terminus of the membrane protein FtsQ with the signal anchor, a tRNA in the P-site and the E.coli SecYEG complex embedded in a E.coli lipid bilayer (Nanodisc). | |||||||||
試料 |
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機能・相同性 | 機能・相同性情報 cell septum assembly / Defective ABCA1 causes TGD / Scavenging by Class B Receptors / HDL clearance / high-density lipoprotein particle receptor binding / spherical high-density lipoprotein particle / positive regulation of hydrolase activity / negative regulation of response to cytokine stimulus / regulation of intestinal cholesterol absorption / protein oxidation ...cell septum assembly / Defective ABCA1 causes TGD / Scavenging by Class B Receptors / HDL clearance / high-density lipoprotein particle receptor binding / spherical high-density lipoprotein particle / positive regulation of hydrolase activity / negative regulation of response to cytokine stimulus / regulation of intestinal cholesterol absorption / protein oxidation / vitamin transport / cholesterol import / high-density lipoprotein particle binding / protein transport by the Sec complex / ABC transporters in lipid homeostasis / intracellular protein transmembrane transport / blood vessel endothelial cell migration / negative regulation of heterotypic cell-cell adhesion / apolipoprotein receptor binding / apolipoprotein A-I receptor binding / negative regulation of cytokine production involved in immune response / negative regulation of cell adhesion molecule production / HDL assembly / negative regulation of very-low-density lipoprotein particle remodeling / peptidyl-methionine modification / phosphatidylcholine biosynthetic process / protein-transporting ATPase activity / glucocorticoid metabolic process / acylglycerol homeostasis / Chylomicron remodeling / phosphatidylcholine-sterol O-acyltransferase activator activity / positive regulation of phospholipid efflux / Chylomicron assembly / positive regulation of cholesterol metabolic process / lipid storage / high-density lipoprotein particle clearance / phospholipid homeostasis / chylomicron / high-density lipoprotein particle remodeling / phospholipid efflux / chemorepellent activity / cholesterol transfer activity / reverse cholesterol transport / very-low-density lipoprotein particle / high-density lipoprotein particle assembly / low-density lipoprotein particle / positive regulation of CoA-transferase activity / lipoprotein biosynthetic process / cholesterol transport / high-density lipoprotein particle / FtsZ-dependent cytokinesis / regulation of Cdc42 protein signal transduction / triglyceride homeostasis / HDL remodeling / endothelial cell proliferation / negative regulation of interleukin-1 beta production / Scavenging by Class A Receptors / cholesterol efflux / negative chemotaxis / positive regulation of cholesterol efflux / positive regulation of Rho protein signal transduction / adrenal gland development / cholesterol binding / cell division site / stringent response / cholesterol biosynthetic process / plasma membrane => GO:0005886 / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / endocytic vesicle / RNA folding / protein secretion / negative regulation of tumor necrosis factor-mediated signaling pathway / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / protein targeting / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / Scavenging of heme from plasma / Retinoid metabolism and transport / four-way junction DNA binding / translational termination / positive regulation of substrate adhesion-dependent cell spreading / DnaA-L2 complex / positive regulation of phagocytosis / translation repressor activity / negative regulation of translational initiation / positive regulation of stress fiber assembly / endocytic vesicle lumen / negative regulation of DNA-templated DNA replication initiation / heat shock protein binding / regulation of mRNA stability / cholesterol metabolic process / mRNA regulatory element binding translation repressor activity / ribosome assembly / positive regulation of RNA splicing / assembly of large subunit precursor of preribosome 類似検索 - 分子機能 | |||||||||
生物種 | Escherichia coli (大腸菌) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 7.1 Å | |||||||||
データ登録者 | Frauenfeld J / Gumbart J / Sluis EO / Funes S / Gartmann M / Beatrix B / Mielke T / Berninghausen O / Becker T / Schulten K / Beckmann R | |||||||||
引用 | ジャーナル: Nat Struct Mol Biol / 年: 2011 タイトル: Cryo-EM structure of the ribosome-SecYE complex in the membrane environment. 著者: Jens Frauenfeld / James Gumbart / Eli O van der Sluis / Soledad Funes / Marco Gartmann / Birgitta Beatrix / Thorsten Mielke / Otto Berninghausen / Thomas Becker / Klaus Schulten / Roland Beckmann / 要旨: The ubiquitous SecY-Sec61 complex translocates nascent secretory proteins across cellular membranes and integrates membrane proteins into lipid bilayers. Several structures of mostly detergent- ...The ubiquitous SecY-Sec61 complex translocates nascent secretory proteins across cellular membranes and integrates membrane proteins into lipid bilayers. Several structures of mostly detergent-solubilized Sec complexes have been reported. Here we present a single-particle cryo-EM structure of the SecYEG complex in a membrane environment, bound to a translating ribosome, at subnanometer resolution. Using the SecYEG complex reconstituted in a so-called Nanodisc, we could trace the nascent polypeptide chain from the peptidyltransferase center into the membrane. The reconstruction allowed for the identification of ribosome-lipid interactions. The rRNA helix 59 (H59) directly contacts the lipid surface and appears to modulate the membrane in immediate vicinity to the proposed lateral gate of the protein-conducting channel (PCC). On the basis of our map and molecular dynamics simulations, we present a model of a signal anchor-gated PCC in the membrane. | |||||||||
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 | EMマップ: SurfViewMolmilJmol/JSmol |
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_1858.map.gz | 8.5 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-1858-v30.xml emd-1858.xml | 9.9 KB 9.9 KB | 表示 表示 | EMDBヘッダ |
画像 | EMD-1858_image.jpg | 322.7 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-1858 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1858 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_1858_validation.pdf.gz | 353.2 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_1858_full_validation.pdf.gz | 352.8 KB | 表示 | |
XML形式データ | emd_1858_validation.xml.gz | 6.7 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1858 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1858 | 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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「今月の分子」の関連する項目 |
-マップ
ファイル | ダウンロード / ファイル: emd_1858.map.gz / 形式: CCP4 / 大きさ: 122.1 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | This map represents an E.coli 70S ribosome carrying an elongation arrested nascent chain of 118 amino acid residues, with the first 102 residues representing the N-terminus of the membrane protein FtsQ with the signal anchor, a tRNA in the P-site and the E.coli SecYEG complex embedded in a E.coli lipid bilayer (Nanodisc). | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.2375 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 : An active E.coli SecYEG complex embedded in a lipid bilayer (Nano...
全体 | 名称: An active E.coli SecYEG complex embedded in a lipid bilayer (Nanodisc), bound to a translating E.coli ribosome |
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要素 |
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-超分子 #1000: An active E.coli SecYEG complex embedded in a lipid bilayer (Nano...
超分子 | 名称: An active E.coli SecYEG complex embedded in a lipid bilayer (Nanodisc), bound to a translating E.coli ribosome タイプ: sample / ID: 1000 詳細: The heterotrimeric SecYEG complex was embedded in a lipid bilayer (nascent HDL, Nanodisc) 集合状態: 70S ribosome bound to one copy of the E.coli SecYEG complex in a lipid bilayer Number unique components: 2 |
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分子量 | 理論値: 2.7 MDa |
-超分子 #1: 70S ribosome nascent chain complex
超分子 | 名称: 70S ribosome nascent chain complex / タイプ: complex / ID: 1 / Name.synonym: 70S RNC / 組換発現: No / Ribosome-details: ribosome-prokaryote: ALL |
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由来(天然) | 生物種: Escherichia coli (大腸菌) |
分子量 | 理論値: 2.7 MDa |
-分子 #1: Nd-SecYEG
分子 | 名称: Nd-SecYEG / タイプ: ligand / ID: 1 / Name.synonym: SecYEG embedded in a Nanodisc / コピー数: 1 / 集合状態: Heterotrimeric / 組換発現: Yes |
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由来(天然) | 生物種: Escherichia coli (大腸菌) / 細胞中の位置: Plasma membrane |
組換発現 | 生物種: Escherichia coli (大腸菌) |
-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 | 単粒子再構成法 |
試料の集合状態 | particle |
-試料調製
緩衝液 | pH: 7.2 詳細: 20 mM Hepes (pH 7.2), 100 mM KOAc, 10 mM Mg(OAc)2, 1 mM DTT, 250 microg/ml chloramphenicol |
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凍結 | 凍結剤: ETHANE / 装置: OTHER |
-電子顕微鏡法
顕微鏡 | FEI POLARA 300 |
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撮影 | カテゴリ: FILM / フィルム・検出器のモデル: KODAK SO-163 FILM / デジタル化 - スキャナー: PRIMESCAN / デジタル化 - サンプリング間隔: 4.76 µm / 平均電子線量: 22 e/Å2 / 詳細: Scanned at 5334 dpi |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 倍率(補正後): 38000 / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2.26 mm / 最大 デフォーカス(公称値): 4.5 µm / 最小 デフォーカス(公称値): 1.0 µm / 倍率(公称値): 39000 |
試料ステージ | 試料ホルダー: FEI Polara cartridge system / 試料ホルダーモデル: OTHER |
実験機器 | モデル: Tecnai Polara / 画像提供: FEI Company |
-画像解析
CTF補正 | 詳細: Defocus group volumes |
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最終 再構成 | 想定した対称性 - 点群: C1 (非対称) / 解像度のタイプ: BY AUTHOR / 解像度: 7.1 Å / 解像度の算出法: FSC 0.5 CUT-OFF / ソフトウェア - 名称: SPIDER / 使用した粒子像数: 85664 |