- EMDB-3068: Mammalian ribosome bound to the native Sec61 protein-conducting c... -
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基本情報
登録情報
データベース: EMDB / ID: EMD-3068
タイトル
Mammalian ribosome bound to the native Sec61 protein-conducting channel in the 'non-inserting' state ('conventional' alignment)
マップデータ
Subtomogram average of non-solubilized ribosome-Sec61 complexes in the 'non-inserting' state. Subtomogram alignment was carried out using 'conventional' alignment.
試料
試料: Mammalian ribosome bound to the native protein translocon on canine pancreatic ER vesicles
Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / membrane docking / endoplasmic reticulum Sec complex / pronephric nephron development / cotranslational protein targeting to membrane / Ssh1 translocon complex / Sec61 translocon complex / protein targeting to ER / protein-transporting ATPase activity / protein insertion into ER membrane ...Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / membrane docking / endoplasmic reticulum Sec complex / pronephric nephron development / cotranslational protein targeting to membrane / Ssh1 translocon complex / Sec61 translocon complex / protein targeting to ER / protein-transporting ATPase activity / protein insertion into ER membrane / signal sequence binding / post-translational protein targeting to membrane, translocation / SRP-dependent cotranslational protein targeting to membrane, translocation / protein transmembrane transporter activity / phospholipid binding / ribosome binding / endoplasmic reticulum membrane / endoplasmic reticulum / membrane 類似検索 - 分子機能
Protein transport Sec61-beta/Sbh / Protein transport protein SecG/Sec61-beta/Sbh / Sec61beta family / Protein translocase SEC61 complex, gamma subunit / Protein translocase SecE domain superfamily / Translocon Sec61/SecY, plug domain / Plug domain of Sec61p / Protein secE/sec61-gamma signature. / Protein secY signature 1. / Protein secY signature 2. ...Protein transport Sec61-beta/Sbh / Protein transport protein SecG/Sec61-beta/Sbh / Sec61beta family / Protein translocase SEC61 complex, gamma subunit / Protein translocase SecE domain superfamily / Translocon Sec61/SecY, plug domain / Plug domain of Sec61p / Protein secE/sec61-gamma signature. / Protein secY signature 1. / Protein secY signature 2. / SecE/Sec61-gamma subunits of protein translocation complex / Protein translocase complex, SecE/Sec61-gamma subunit / SecY/SEC61-alpha family / SecY domain superfamily / SecY conserved site / SecY 類似検索 - ドメイン・相同性
Protein transport protein Sec61 subunit alpha isoform 1 / Protein transport protein Sec61 subunit gamma / Protein transport protein Sec61 subunit beta 類似検索 - 構成要素
ジャーナル: Nat Commun / 年: 2015 タイトル: Structure of the native Sec61 protein-conducting channel. 著者: Stefan Pfeffer / Laura Burbaum / Pia Unverdorben / Markus Pech / Yuxiang Chen / Richard Zimmermann / Roland Beckmann / Friedrich Förster / 要旨: In mammalian cells, secretory and membrane proteins are translocated across or inserted into the endoplasmic reticulum (ER) membrane by the universally conserved protein-conducting channel Sec61, ...In mammalian cells, secretory and membrane proteins are translocated across or inserted into the endoplasmic reticulum (ER) membrane by the universally conserved protein-conducting channel Sec61, which has been structurally studied in isolated, detergent-solubilized states. Here we structurally and functionally characterize native, non-solubilized ribosome-Sec61 complexes on rough ER vesicles using cryo-electron tomography and ribosome profiling. Surprisingly, the 9-Å resolution subtomogram average reveals Sec61 in a laterally open conformation, even though the channel is not in the process of inserting membrane proteins into the lipid bilayer. In contrast to recent mechanistic models for polypeptide translocation and insertion, our results indicate that the laterally open conformation of Sec61 is the only conformation present in the ribosome-bound translocon complex, independent of its functional state. Consistent with earlier functional studies, our structure suggests that the ribosome alone, even without a nascent chain, is sufficient for lateral opening of Sec61 in a lipid environment.
ダウンロード / ファイル: emd_3068.map.gz / 形式: CCP4 / 大きさ: 39.7 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
注釈
Subtomogram average of non-solubilized ribosome-Sec61 complexes in the 'non-inserting' state. Subtomogram alignment was carried out using 'conventional' alignment.
ボクセルのサイズ
X=Y=Z: 2.62 Å
密度
表面レベル
登録者による: 3.0 / ムービー #1: 3
最小 - 最大
-16.746192929999999 - 20.314157489999999
平均 (標準偏差)
0.0 (±0.99999994)
対称性
空間群: 1
詳細
EMDB XML:
マップ形状
Axis order
X
Y
Z
Origin
0
0
0
サイズ
220
220
220
Spacing
220
220
220
セル
A=B=C: 576.39996 Å α=β=γ: 90.0 °
CCP4マップ ヘッダ情報:
mode
Image stored as Reals
Å/pix. X/Y/Z
2.62
2.62
2.62
M x/y/z
220
220
220
origin x/y/z
0.000
0.000
0.000
length x/y/z
576.400
576.400
576.400
α/β/γ
90.000
90.000
90.000
MAP C/R/S
1
2
3
start NC/NR/NS
0
0
0
NC/NR/NS
220
220
220
D min/max/mean
-16.746
20.314
0.000
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添付データ
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試料の構成要素
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全体 : Mammalian ribosome bound to the native protein translocon on cani...
全体
名称: Mammalian ribosome bound to the native protein translocon on canine pancreatic ER vesicles
要素
試料: Mammalian ribosome bound to the native protein translocon on canine pancreatic ER vesicles
複合体: Membrane-bound 80S ribosome
タンパク質・ペプチド: ER protein translocon
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超分子 #1000: Mammalian ribosome bound to the native protein translocon on cani...
超分子
名称: Mammalian ribosome bound to the native protein translocon on canine pancreatic ER vesicles タイプ: sample / ID: 1000 / Number unique components: 2
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超分子 #1: Membrane-bound 80S ribosome
超分子
名称: Membrane-bound 80S ribosome / タイプ: complex / ID: 1 / 組換発現: No / Ribosome-details: ribosome-eukaryote: ALL
試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER Tilt series - Axis1 - Min angle: -20 ° / Tilt series - Axis1 - Max angle: 20 °
実験機器
モデル: Titan Krios / 画像提供: FEI Company
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画像解析
詳細
Tomogram reconstruction and template matching against a single particle cryo-EM reconstruction of the 80S ribosome were accomplished using PyTom. Subtomograms extracted from cross correlation peaks in the tomogram were classified using constrained principal component analysis focusing on the large ribosomal subunit and the ER membrane. For the retained coordinates, 1 x binned subtomograms were reconstructed individually from the weighted back-projections using the full tilt range, iteratively aligned and classified focusing on the translocon. For the retained coordinates, unbinned subtomograms were reconstructed individually from the weighted back-projections using only a reduced tilt range (-20 deg to +20 deg) and iteratively aligned using a 'conventional' subtomogram alignment procedure.
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: 9.0 Å / 解像度の算出法: OTHER ソフトウェア - 名称: PyTom, tom_toolbox, av3_toolbox 使用したサブトモグラム数: 17600