+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-4743 | ||||||||||||
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タイトル | Ribosome-bound SecYEG translocon in a nanodisc | ||||||||||||
マップデータ | SecYEG:Nanodisc portion of the RNC:SecYEG:Nanodisc complex after multi-body refinement. | ||||||||||||
試料 |
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機能・相同性 | 機能・相同性情報 protein insertion into membrane from inner side / cell envelope Sec protein transport complex / protein transport by the Sec complex / intracellular protein transmembrane transport / protein-transporting ATPase activity / SRP-dependent cotranslational protein targeting to membrane, translocation / signal sequence binding / protein transmembrane transporter activity / protein secretion / protein targeting ...protein insertion into membrane from inner side / cell envelope Sec protein transport complex / protein transport by the Sec complex / intracellular protein transmembrane transport / protein-transporting ATPase activity / SRP-dependent cotranslational protein targeting to membrane, translocation / signal sequence binding / protein transmembrane transporter activity / protein secretion / protein targeting / intracellular protein transport / membrane => GO:0016020 / 生体膜 / 細胞膜 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: 6.0 Å | ||||||||||||
データ登録者 | Kater L / Beckmann R / Kedrov A | ||||||||||||
資金援助 | ドイツ, 3件
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引用 | ジャーナル: EMBO Rep / 年: 2019 タイトル: Partially inserted nascent chain unzips the lateral gate of the Sec translocon. 著者: Lukas Kater / Benedikt Frieg / Otto Berninghausen / Holger Gohlke / Roland Beckmann / Alexej Kedrov / 要旨: The Sec translocon provides the lipid bilayer entry for ribosome-bound nascent chains and thus facilitates membrane protein biogenesis. Despite the appreciated role of the native environment in the ...The Sec translocon provides the lipid bilayer entry for ribosome-bound nascent chains and thus facilitates membrane protein biogenesis. Despite the appreciated role of the native environment in the translocon:ribosome assembly, structural information on the complex in the lipid membrane is scarce. Here, we present a cryo-electron microscopy-based structure of bacterial translocon SecYEG in lipid nanodiscs and elucidate an early intermediate state upon insertion of the FtsQ anchor domain. Insertion of the short nascent chain causes initial displacements within the lateral gate of the translocon, where α-helices 2b, 7, and 8 tilt within the membrane core to "unzip" the gate at the cytoplasmic side. Molecular dynamics simulations demonstrate that the conformational change is reversed in the absence of the ribosome, and suggest that the accessory α-helices of SecE subunit modulate the lateral gate conformation. Site-specific cross-linking validates that the FtsQ nascent chain passes the lateral gate upon insertion. The structure and the biochemical data suggest that the partially inserted nascent chain remains highly flexible until it acquires the transmembrane topology. | ||||||||||||
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_4743.map.gz | 1.3 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-4743-v30.xml emd-4743.xml | 17.7 KB 17.7 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_4743_fsc.xml | 3 KB | 表示 | FSCデータファイル |
画像 | emd_4743.png | 118.1 KB | ||
その他 | emd_4743_additional_1.map.gz emd_4743_additional_2.map.gz | 95.8 MB 197.3 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-4743 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4743 | 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_4743.map.gz / 形式: CCP4 / 大きさ: 2 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | SecYEG:Nanodisc portion of the RNC:SecYEG:Nanodisc complex after multi-body refinement. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 2.168 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
-追加マップ: Large ribosomal subunit portion of the RNC:SecYEG:Nanodisc complex...
ファイル | emd_4743_additional_1.map | ||||||||||||
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注釈 | Large ribosomal subunit portion of the RNC:SecYEG:Nanodisc complex after multi-body refinement. This map includes the tRNA, nascent chain, SecYEG and nanodisc. Filtered according to local resolution. | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: Large ribosomal subunit portion of the RNC:SecYEG:Nanodisc complex...
ファイル | emd_4743_additional_2.map | ||||||||||||
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注釈 | Large ribosomal subunit portion of the RNC:SecYEG:Nanodisc complex after multi-body refinement. This map includes the tRNA, nascent chain, SecYEG and nanodisc. Filtered according to local resolution. | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-試料の構成要素
-全体 : Stalled E. coli ribosome nascent chain complex (RNC) bound to the...
全体 | 名称: Stalled E. coli ribosome nascent chain complex (RNC) bound to the translocon SecYEG in a nanodisc |
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要素 |
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-超分子 #1: Stalled E. coli ribosome nascent chain complex (RNC) bound to the...
超分子 | 名称: Stalled E. coli ribosome nascent chain complex (RNC) bound to the translocon SecYEG in a nanodisc タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: all |
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由来(天然) | 生物種: Escherichia coli (大腸菌) |
-分子 #1: SecG
分子 | 名称: SecG / タイプ: protein_or_peptide / ID: 1 / コピー数: 1 / 光学異性体: LEVO |
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由来(天然) | 生物種: Escherichia coli (大腸菌) |
分子量 | 理論値: 1.890321 KDa |
配列 | 文字列: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK) |
-分子 #2: SecE,Protein translocase subunit SecE,Protein translocase subunit...
分子 | 名称: SecE,Protein translocase subunit SecE,Protein translocase subunit SecE,Protein translocase subunit SecE タイプ: protein_or_peptide / ID: 2 / コピー数: 1 / 光学異性体: LEVO |
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由来(天然) | 生物種: Escherichia coli (大腸菌) |
分子量 | 理論値: 10.880122 KDa |
配列 | 文字列: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) ...文字列: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)LLTTKGKAT VAFAREARTE VRKVIWPTRQ ETLHTTLIVA AVTAVM SLI LWGLDGILVR LVSFITGLRF |
-分子 #3: Protein translocase subunit SecY
分子 | 名称: Protein translocase subunit SecY / タイプ: protein_or_peptide / ID: 3 / コピー数: 1 / 光学異性体: LEVO |
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由来(天然) | 生物種: Escherichia coli (大腸菌) |
分子量 | 理論値: 48.553375 KDa |
配列 | 文字列: MAKQPGLDFQ SAKGGLGELK RRLLFVIGAL IVFRIGSFIP IPGIDAAVLA KLLEQQRGTI IEMFNMFSGG ALSRASIFAL GIMPYISAS IIIQLLTVVH PTLAEIKKEG ESGRRKISQY TRYGTLVLAI FQSIGIATGL PNMPGMQGLV INPGFAFYFT A VVSLVTGT ...文字列: MAKQPGLDFQ SAKGGLGELK RRLLFVIGAL IVFRIGSFIP IPGIDAAVLA KLLEQQRGTI IEMFNMFSGG ALSRASIFAL GIMPYISAS IIIQLLTVVH PTLAEIKKEG ESGRRKISQY TRYGTLVLAI FQSIGIATGL PNMPGMQGLV INPGFAFYFT A VVSLVTGT MFLMWLGEQI TERGIGNGIS IIIFAGIVAG LPPAIAHTIE QARQGDLHFL VLLLVAVLVF AVTFFVVFVE RG QRRIVVN YAKRQQGRRV YAAQSTHLPL KVNMAGVIPA IFASSIILFP ATIASWFGGG TGWNWLTTIS LYLQPGQPLY VLL YASAII FFCFFYTALV FNPRETADNL KKSGAFVPGI RPGEQTAKYI DKVMTRLTLV GALYITFICL IPEFMRDAMK VPFY FGGTS LLIVVVVIMD FMAQVQTLMM SSQYESALKK ANLKGYGR |
-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: 7.4 |
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凍結 | 凍結剤: ETHANE |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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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 FIELDBright-field microscopy |
撮影 | フィルム・検出器のモデル: FEI FALCON II (4k x 4k) 検出モード: INTEGRATING / デジタル化 - サイズ - 横: 4096 pixel / デジタル化 - サイズ - 縦: 4096 pixel / 実像数: 13098 / 平均電子線量: 2.5 e/Å2 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |