+
データを開く
-
基本情報
登録情報 | ![]() | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
タイトル | Subtomogram average of the human Sec61-TRAP-OSTA-translocon | ||||||||||||
![]() | subtomogram average of the Sec61-TRAP-OSTA translocon | ||||||||||||
![]() |
| ||||||||||||
![]() | membrane protein complex / protein translocation / N-glycosylation / signal peptide insertion / MEMBRANE PROTEIN | ||||||||||||
機能・相同性 | ![]() oligosaccharyltransferase complex binding / oligosaccharyltransferase complex A / oligosaccharyltransferase complex B / Asparagine N-linked glycosylation / endoplasmic reticulum Sec complex / pronephric nephron development / dolichyl-diphosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / oligosaccharyltransferase complex / endoplasmic reticulum quality control compartment ...oligosaccharyltransferase complex binding / oligosaccharyltransferase complex A / oligosaccharyltransferase complex B / Asparagine N-linked glycosylation / endoplasmic reticulum Sec complex / pronephric nephron development / dolichyl-diphosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / oligosaccharyltransferase complex / endoplasmic reticulum quality control compartment / cotranslational protein targeting to membrane / Ssh1 translocon complex / Sec61 translocon complex / protein targeting to ER / protein insertion into ER membrane / post-translational protein targeting to endoplasmic reticulum membrane / protein N-linked glycosylation via asparagine / : / XBP1(S) activates chaperone genes / SRP-dependent cotranslational protein targeting to membrane, translocation / signal sequence binding / SRP-dependent cotranslational protein targeting to membrane / protein N-linked glycosylation / post-translational protein targeting to membrane, translocation / endoplasmic reticulum organization / epithelial cell apoptotic process / azurophil granule membrane / epidermal growth factor binding / retrograde protein transport, ER to cytosol / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / protein glycosylation / Advanced glycosylation endproduct receptor signaling / SRP-dependent cotranslational protein targeting to membrane / protein transmembrane transporter activity / blastocyst development / response to type II interferon / rough endoplasmic reticulum / ERAD pathway / response to cytokine / endomembrane system / post-translational protein modification / response to endoplasmic reticulum stress / T cell activation / guanyl-nucleotide exchange factor activity / enzyme activator activity / protein modification process / regulation of protein stability / calcium channel activity / melanosome / ribosome binding / ER-Phagosome pathway / protein-macromolecule adaptor activity / Maturation of spike protein / in utero embryonic development / nuclear body / inflammatory response / intracellular membrane-bounded organelle / apoptotic process / positive regulation of cell population proliferation / Neutrophil degranulation / endoplasmic reticulum membrane / negative regulation of apoptotic process / endoplasmic reticulum / RNA binding / extracellular exosome / metal ion binding / membrane / plasma membrane / cytosol / cytoplasm 類似検索 - 分子機能 | ||||||||||||
生物種 | ![]() | ||||||||||||
手法 | サブトモグラム平均法 / クライオ電子顕微鏡法 / 解像度: 7.6 Å | ||||||||||||
![]() | Gemmer M / Fedry JMM / Forster FG | ||||||||||||
資金援助 | European Union, ![]()
| ||||||||||||
![]() | ![]() タイトル: Visualization of translation and protein biogenesis at the ER membrane. 著者: Max Gemmer / Marten L Chaillet / Joyce van Loenhout / Rodrigo Cuevas Arenas / Dimitrios Vismpas / Mariska Gröllers-Mulderij / Fujiet A Koh / Pascal Albanese / Richard A Scheltema / Stuart C ...著者: Max Gemmer / Marten L Chaillet / Joyce van Loenhout / Rodrigo Cuevas Arenas / Dimitrios Vismpas / Mariska Gröllers-Mulderij / Fujiet A Koh / Pascal Albanese / Richard A Scheltema / Stuart C Howes / Abhay Kotecha / Juliette Fedry / Friedrich Förster / ![]() 要旨: The dynamic ribosome-translocon complex, which resides at the endoplasmic reticulum (ER) membrane, produces a major fraction of the human proteome. It governs the synthesis, translocation, membrane ...The dynamic ribosome-translocon complex, which resides at the endoplasmic reticulum (ER) membrane, produces a major fraction of the human proteome. It governs the synthesis, translocation, membrane insertion, N-glycosylation, folding and disulfide-bond formation of nascent proteins. Although individual components of this machinery have been studied at high resolution in isolation, insights into their interplay in the native membrane remain limited. Here we use cryo-electron tomography, extensive classification and molecular modelling to capture snapshots of mRNA translation and protein maturation at the ER membrane at molecular resolution. We identify a highly abundant classical pre-translocation intermediate with eukaryotic elongation factor 1a (eEF1a) in an extended conformation, suggesting that eEF1a may remain associated with the ribosome after GTP hydrolysis during proofreading. At the ER membrane, distinct polysomes bind to different ER translocons specialized in the synthesis of proteins with signal peptides or multipass transmembrane proteins with the translocon-associated protein complex (TRAP) present in both. The near-complete atomic model of the most abundant ER translocon variant comprising the protein-conducting channel SEC61, TRAP and the oligosaccharyltransferase complex A (OSTA) reveals specific interactions of TRAP with other translocon components. We observe stoichiometric and sub-stoichiometric cofactors associated with OSTA, which are likely to include protein isomerases. In sum, we visualize ER-bound polysomes with their coordinated downstream machinery. | ||||||||||||
履歴 |
|
-
構造の表示
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 | ![]() | 149.7 MB | ![]() | |
---|---|---|---|---|
ヘッダ (付随情報) | ![]() ![]() | 34.1 KB 34.1 KB | 表示 表示 | ![]() |
画像 | ![]() | 94.6 KB | ||
Filedesc metadata | ![]() | 9.4 KB | ||
その他 | ![]() ![]() | 82.5 MB 82.5 MB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-検証レポート
文書・要旨 | ![]() | 1 MB | 表示 | ![]() |
---|---|---|---|---|
文書・詳細版 | ![]() | 1 MB | 表示 | |
XML形式データ | ![]() | 13.9 KB | 表示 | |
CIF形式データ | ![]() | 16.8 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
関連構造データ | ![]() 8b6lMC ![]() 8b6zC M: このマップから作成された原子モデル C: 同じ文献を引用 ( |
---|---|
類似構造データ | 類似検索 - 機能・相同性 ![]() |
-
リンク
EMDBのページ | ![]() ![]() |
---|---|
「今月の分子」の関連する項目 |
-
マップ
ファイル | ![]() | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | subtomogram average of the Sec61-TRAP-OSTA translocon | ||||||||||||||||||||||||||||||||||||
投影像・断面図 | 画像のコントロール
画像は Spider により作成 | ||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.724 Å | ||||||||||||||||||||||||||||||||||||
密度 |
| ||||||||||||||||||||||||||||||||||||
対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
|
-添付データ
-ハーフマップ: subtomogram average of the Sec61-TRAP-OSTA translocon
ファイル | emd_15870_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | subtomogram average of the Sec61-TRAP-OSTA translocon | ||||||||||||
投影像・断面図 |
| ||||||||||||
密度ヒストグラム |
-ハーフマップ: subtomogram average of the Sec61-TRAP-OSTA translocon
ファイル | emd_15870_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | subtomogram average of the Sec61-TRAP-OSTA translocon | ||||||||||||
投影像・断面図 |
| ||||||||||||
密度ヒストグラム |
-
試料の構成要素
+全体 : Sec61-TRAP-OSTA translocon complex
+超分子 #1: Sec61-TRAP-OSTA translocon complex
+分子 #1: Protein transport protein Sec61 subunit alpha isoform 1
+分子 #2: Protein transport protein Sec61 subunit beta
+分子 #3: Protein transport protein Sec61 subunit gamma
+分子 #4: Signal peptide mix
+分子 #5: Translocon-associated protein subunit alpha
+分子 #6: Translocon-associated protein subunit beta
+分子 #7: Translocon-associated protein subunit gamma
+分子 #8: Translocon-associated protein subunit delta
+分子 #9: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase su...
+分子 #10: Oligosaccharyltransferase complex subunit OSTC
+分子 #11: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase su...
+分子 #12: Transmembrane protein 258
+分子 #13: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase su...
+分子 #14: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48...
+分子 #15: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase su...
+分子 #16: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase su...
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
---|---|
![]() | サブトモグラム平均法 |
試料の集合状態 | particle |
-
試料調製
濃度 | 2 mg/mL |
---|---|
緩衝液 | pH: 7.4 |
グリッド | モデル: Quantifoil / 材質: COPPER / 前処理 - タイプ: GLOW DISCHARGE / 前処理 - 時間: 30 sec. |
凍結 | 凍結剤: ETHANE-PROPANE / 詳細: Manual plunger. |
詳細 | ER-derived vesicles decorated with cytosolic ribosomes. |
-
電子顕微鏡法
顕微鏡 | FEI TALOS ARCTICA |
---|---|
撮影 | フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 検出モード: COUNTING / デジタル化 - 画像ごとのフレーム数: 7-7 / 撮影したグリッド数: 8 / 平均露光時間: 0.7 sec. / 平均電子線量: 2.3 e/Å2 |
電子線 | 加速電圧: 200 kV / 電子線源: ![]() |
電子光学系 | C2レンズ絞り径: 100.0 µm / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2.7 mm / 最大 デフォーカス(公称値): 3.0 µm / 最小 デフォーカス(公称値): 3.0 µm / 倍率(公称値): 79000 |
試料ステージ | ホルダー冷却材: NITROGEN |
実験機器 | ![]() モデル: Talos Arctica / 画像提供: FEI Company |
-
画像解析
最終 再構成 | アルゴリズム: BACK PROJECTION / 解像度のタイプ: BY AUTHOR / 解像度: 7.6 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用したサブトモグラム数: 42215 |
---|---|
抽出 | トモグラム数: 869 / 使用した粒子像数: 134350 参照モデル: Subtomogram average of ER membrane-associated ribosome 手法: Template matching / ソフトウェア - 名称: PyTom (ver. 0.994) |
最終 3次元分類 | ソフトウェア - 名称: RELION (ver. 3.1.1) |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD / ソフトウェア - 名称: RELION (ver. 3.1.1) |
-原子モデル構築 1
精密化 | 空間: REAL / プロトコル: FLEXIBLE FIT |
---|---|
得られたモデル | ![]() PDB-8b6l: |