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- EMDB-4161: Cryo-EM structure of the yeast oligosaccharyltransferase (OST) complex -
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データを開く
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基本情報
登録情報 | データベース: EMDB / ID: EMD-4161 | |||||||||
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タイトル | Cryo-EM structure of the yeast oligosaccharyltransferase (OST) complex | |||||||||
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機能・相同性 | ![]() Miscellaneous transport and binding events / oligosaccharyltransferase I complex / protein O-linked mannosylation / oligosaccharyltransferase complex / dolichyl-diphosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / protein N-linked glycosylation via asparagine / protein N-linked glycosylation / glycosyltransferase activity / protein glycosylation ...Miscellaneous transport and binding events / oligosaccharyltransferase I complex / protein O-linked mannosylation / oligosaccharyltransferase complex / dolichyl-diphosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / protein N-linked glycosylation via asparagine / protein N-linked glycosylation / glycosyltransferase activity / protein glycosylation / protein-disulfide reductase activity / Neutrophil degranulation / post-translational protein modification / protein-macromolecule adaptor activity / nuclear envelope / protein-containing complex assembly / endoplasmic reticulum membrane / endoplasmic reticulum / mitochondrion / membrane / metal ion binding 類似検索 - 分子機能 | |||||||||
生物種 | ![]() ![]() ![]() ![]() | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.3 Å | |||||||||
![]() | Wild R / Kowal J / Eyring J / Ngwa EM / Aebi M / Locher KP | |||||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Structure of the yeast oligosaccharyltransferase complex gives insight into eukaryotic N-glycosylation. 著者: Rebekka Wild / Julia Kowal / Jillianne Eyring / Elsy M Ngwa / Markus Aebi / Kaspar P Locher / ![]() 要旨: Oligosaccharyltransferase (OST) is an essential membrane protein complex in the endoplasmic reticulum, where it transfers an oligosaccharide from a dolichol-pyrophosphate-activated donor to ...Oligosaccharyltransferase (OST) is an essential membrane protein complex in the endoplasmic reticulum, where it transfers an oligosaccharide from a dolichol-pyrophosphate-activated donor to glycosylation sites of secretory proteins. Here we describe the atomic structure of yeast OST determined by cryo-electron microscopy, revealing a conserved subunit arrangement. The active site of the catalytic STT3 subunit points away from the center of the complex, allowing unhindered access to substrates. The dolichol-pyrophosphate moiety binds to a lipid-exposed groove of STT3, whereas two noncatalytic subunits and an ordered N-glycan form a membrane-proximal pocket for the oligosaccharide. The acceptor polypeptide site faces an oxidoreductase domain in stand-alone OST complexes or is immediately adjacent to the translocon, suggesting how eukaryotic OSTs efficiently glycosylate a large number of polypeptides before their folding. | |||||||||
履歴 |
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構造の表示
ムービー |
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構造ビューア | EMマップ: ![]() ![]() ![]() |
添付画像 |
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ダウンロードとリンク
-EMDBアーカイブ
マップデータ | ![]() | 62.8 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 29 KB 29 KB | 表示 表示 | ![]() |
FSC (解像度算出) | ![]() | 10.5 KB | 表示 | ![]() |
画像 | ![]() | 50.2 KB | ||
その他 | ![]() ![]() | 7.6 MB 96.6 MB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-検証レポート
文書・要旨 | ![]() | 376.9 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 376.5 KB | 表示 | |
XML形式データ | ![]() | 11.8 KB | 表示 | |
CIF形式データ | ![]() | 15.6 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
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リンク
EMDBのページ | ![]() ![]() |
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「今月の分子」の関連する項目 |
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マップ
ファイル | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | None | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.065 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: Map of OST complex in nanodisc, post-processed and masked
ファイル | emd_4161_additional_1.map | ||||||||||||
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注釈 | Map of OST complex in nanodisc, post-processed and masked | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: Map of OST complex, after nanodisc subtraction, post-processed
ファイル | emd_4161_additional_2.map | ||||||||||||
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注釈 | Map of OST complex, after nanodisc subtraction, post-processed | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
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試料の構成要素
+全体 : yeast oligosaccharyltransferase (OST) complex
+超分子 #1: yeast oligosaccharyltransferase (OST) complex
+分子 #1: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase su...
+分子 #2: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase su...
+分子 #3: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase su...
+分子 #4: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase su...
+分子 #5: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase su...
+分子 #6: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase su...
+分子 #7: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase su...
+分子 #8: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase su...
+分子 #12: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
+分子 #13: PHOSPHATIDYLETHANOLAMINE
+分子 #14: 2-acetamido-2-deoxy-beta-D-glucopyranose
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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![]() | 単粒子再構成法 |
試料の集合状態 | particle |
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試料調製
濃度 | 0.5 mg/mL |
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緩衝液 | pH: 7.5 / 詳細: 20 mM HEPES, pH 7.5, 150 mM NaCl |
グリッド | モデル: Quantifoil R1.2/1.3 / 材質: COPPER / メッシュ: 300 / 前処理 - タイプ: GLOW DISCHARGE / 前処理 - 時間: 40 sec. |
凍結 | 凍結剤: ETHANE-PROPANE / チャンバー内湿度: 95 % / チャンバー内温度: 277 K / 装置: FEI VITROBOT MARK IV 詳細: Quantifoil carbon grids (300 mesh, copper) were glow discharged at 25 mA for 40 s. 3.5 ul of nanodisc-reconstituted OST sample at concentration of 0.5 mg/ml was applied onto the grid and ...詳細: Quantifoil carbon grids (300 mesh, copper) were glow discharged at 25 mA for 40 s. 3.5 ul of nanodisc-reconstituted OST sample at concentration of 0.5 mg/ml was applied onto the grid and grids were blotted for 3 s and flash-frozen in a mixture of liquid ethane and propane cooled by liquid nitrogen.. |
詳細 | OST complex reconstituted into nanodisc |
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電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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特殊光学系 | エネルギーフィルター - 名称: GIF Quantum LS |
撮影 | フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 撮影したグリッド数: 2 / 実像数: 3915 / 平均露光時間: 0.25 sec. / 平均電子線量: 2.0 e/Å2 |
電子線 | 加速電圧: 300 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 |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER ホルダー冷却材: NITROGEN |
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |
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画像解析
-原子モデル構築 1
精密化 | プロトコル: AB INITIO MODEL |
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得られたモデル | ![]() PDB-6ezn: |