+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 6w6l | ||||||||||||||||||
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タイトル | Cryo-EM structure of the human ribosome-TMCO1 translocon | ||||||||||||||||||
要素 |
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キーワード | RIBOSOME/PROTEIN TRANSPORT / RIBOSOME-PROTEIN TRANSPORT complex | ||||||||||||||||||
機能・相同性 | 機能・相同性情報 : / negative regulation of nodal signaling pathway / : / multi-pass transmembrane protein insertion into ER membrane / multi-pass translocon complex / endoplasmic reticulum Sec complex / protein localization to nuclear inner membrane / determination of left/right asymmetry in lateral mesoderm / pronephric nephron development / rough endoplasmic reticulum membrane ...: / negative regulation of nodal signaling pathway / : / multi-pass transmembrane protein insertion into ER membrane / multi-pass translocon complex / endoplasmic reticulum Sec complex / protein localization to nuclear inner membrane / determination of left/right asymmetry in lateral mesoderm / pronephric nephron development / rough endoplasmic reticulum membrane / 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 / regulation of protein complex stability / post-translational protein targeting to endoplasmic reticulum membrane / eukaryotic 80S initiation complex / endoplasmic reticulum calcium ion homeostasis / negative regulation of protein neddylation / SRP-dependent cotranslational protein targeting to membrane, translocation / translation at presynapse / axial mesoderm development / embryonic brain development / negative regulation of formation of translation preinitiation complex / 90S preribosome assembly / SRP-dependent cotranslational protein targeting to membrane / signal sequence binding / post-translational protein targeting to membrane, translocation / endoplasmic reticulum organization / GAIT complex / middle ear morphogenesis / A band / alpha-beta T cell differentiation / cytoplasmic side of rough endoplasmic reticulum membrane / retrograde protein transport, ER to cytosol / exit from mitosis / epidermal growth factor binding / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of translation involved in cellular response to UV / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / negative regulation of ubiquitin protein ligase activity / optic nerve development / response to aldosterone / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / retinal ganglion cell axon guidance / homeostatic process / ER overload response / macrophage chemotaxis / lung morphogenesis / Protein hydroxylation / Peptide chain elongation / Selenocysteine synthesis / positive regulation of signal transduction by p53 class mediator / Formation of a pool of free 40S subunits / blastocyst development / ubiquitin ligase inhibitor activity / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / protein transmembrane transporter activity / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / protein localization to nucleus / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / regulation of protein-containing complex assembly / regulation of signal transduction / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / protein targeting / cellular response to interleukin-4 / protein-RNA complex assembly / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of ubiquitin-dependent protein catabolic process / translation regulator activity / ERAD pathway / rough endoplasmic reticulum / MDM2/MDM4 family protein binding / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / maturation of LSU-rRNA / cytosolic ribosome / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / embryo implantation / bone development / post-embryonic development / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ossification / ribosomal large subunit biogenesis / guanyl-nucleotide exchange factor activity / regulation of signal transduction by p53 class mediator / innate immune response in mucosa / skeletal system development / positive regulation of translation / mRNA 3'-UTR binding / calcium ion transmembrane transport / membrane => GO:0016020 / sensory perception of sound / calcium channel activity / cellular response to type II interferon 類似検索 - 分子機能 | ||||||||||||||||||
生物種 | Homo sapiens (ヒト) | ||||||||||||||||||
手法 | 電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.84 Å | ||||||||||||||||||
データ登録者 | Keenan, R.J. / McGilvray, P.T. | ||||||||||||||||||
資金援助 | 米国, 5件
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引用 | ジャーナル: Elife / 年: 2020 タイトル: An ER translocon for multi-pass membrane protein biogenesis. 著者: Philip T McGilvray / S Andrei Anghel / Arunkumar Sundaram / Frank Zhong / Michael J Trnka / James R Fuller / Hong Hu / Alma L Burlingame / Robert J Keenan / 要旨: Membrane proteins with multiple transmembrane domains play critical roles in cell physiology, but little is known about the machinery coordinating their biogenesis at the endoplasmic reticulum. Here ...Membrane proteins with multiple transmembrane domains play critical roles in cell physiology, but little is known about the machinery coordinating their biogenesis at the endoplasmic reticulum. Here we describe a ~ 360 kDa ribosome-associated complex comprising the core Sec61 channel and five accessory factors: TMCO1, CCDC47 and the Nicalin-TMEM147-NOMO complex. Cryo-electron microscopy reveals a large assembly at the ribosome exit tunnel organized around a central membrane cavity. Similar to protein-conducting channels that facilitate movement of transmembrane segments, cytosolic and luminal funnels in TMCO1 and TMEM147, respectively, suggest routes into the central membrane cavity. High-throughput mRNA sequencing shows selective translocon engagement with hundreds of different multi-pass membrane proteins. Consistent with a role in multi-pass membrane protein biogenesis, cells lacking different accessory components show reduced levels of one such client, the glutamate transporter EAAT1. These results identify a new human translocon and provide a molecular framework for understanding its role in multi-pass membrane protein biogenesis. | ||||||||||||||||||
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 | 分子: MolmilJmol/JSmol |
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 6w6l.cif.gz | 5.4 MB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb6w6l.ent.gz | 表示 | PDB形式 | |
PDBx/mmJSON形式 | 6w6l.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
文書・要旨 | 6w6l_validation.pdf.gz | 1.4 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 6w6l_full_validation.pdf.gz | 1.5 MB | 表示 | |
XML形式データ | 6w6l_validation.xml.gz | 243.2 KB | 表示 | |
CIF形式データ | 6w6l_validation.cif.gz | 430.7 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/w6/6w6l ftp://data.pdbj.org/pub/pdb/validation_reports/w6/6w6l | HTTPS FTP |
-関連構造データ
-リンク
-集合体
登録構造単位 |
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1 |
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-要素
+60S ribosomal protein ... , 41種, 41分子 ABCFGHIJKLMNOPQRSTUVWXYZabcdef...
-RNA鎖 , 5種, 5分子 DEtuv
#4: RNA鎖 | 分子量: 50449.812 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: GenBank: 555853 |
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#5: RNA鎖 | 分子量: 38385.750 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) |
#44: RNA鎖 | 分子量: 1159525.750 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) |
#45: RNA鎖 | 分子量: 24414.451 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) |
#46: RNA鎖 | 分子量: 24436.508 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) |
-タンパク質・ペプチド , 1種, 1分子 y
#47: タンパク質・ペプチド | 分子量: 2315.846 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) |
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-Protein transport protein Sec61 subunit ... , 3種, 3分子 123
#48: タンパク質 | 分子量: 52295.379 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: P61619 |
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#49: タンパク質 | 分子量: 7752.325 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: P60059 |
#50: タンパク質 | 分子量: 9987.456 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: P60468 |
-タンパク質 , 4種, 4分子 4576
#51: タンパク質 | 分子量: 25279.848 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q9BVK8 |
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#52: タンパク質 | 分子量: 63047.145 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q969V3 |
#53: タンパク質 | 分子量: 55946.762 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q96A33 |
#54: タンパク質 | 分子量: 21205.008 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q9UM00 |
-非ポリマー , 3種, 32分子
#55: 化合物 | ChemComp-MG / #56: 化合物 | #57: 水 | ChemComp-HOH / | |
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-詳細
研究の焦点であるリガンドがあるか | N |
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-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
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EM実験 | 試料の集合状態: PARTICLE / 3次元再構成法: 単粒子再構成法 |
-試料調製
構成要素 | 名称: human ribosome-TMCO1 translocon / タイプ: COMPLEX / Entity ID: #1-#54 / 由来: NATURAL | |||||||||||||||||||||||||
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分子量 | 値: 4 MDa / 実験値: NO | |||||||||||||||||||||||||
由来(天然) | 生物種: Homo sapiens (ヒト) | |||||||||||||||||||||||||
緩衝液 | pH: 7.4 | |||||||||||||||||||||||||
緩衝液成分 |
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試料 | 濃度: 0.4 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES / 詳細: The sample was well dispersed on a thin carbon film | |||||||||||||||||||||||||
試料支持 | グリッドの材料: COPPER / グリッドのサイズ: 200 divisions/in. / グリッドのタイプ: C-flat-1.2/1.3 | |||||||||||||||||||||||||
急速凍結 | 装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE / 湿度: 100 % / 凍結前の試料温度: 298 K 詳細: Two filter papers were added to each arm, 2.5 microliters of sample were added to the grids, and 0.5 seconds of drain time was allowed before vitrification. |
-電子顕微鏡撮影
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TITAN KRIOS |
電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELD |
撮影 | 平均露光時間: 3.8 sec. / 電子線照射量: 50 e/Å2 / フィルム・検出器のモデル: GATAN K3 (6k x 4k) / 撮影したグリッド数: 1 / 実像数: 5562 |
-解析
EMソフトウェア |
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
粒子像の選択 | 選択した粒子像数: 1049128 | ||||||||||||||||||||||||||||||||||||||||
対称性 | 点対称性: C1 (非対称) | ||||||||||||||||||||||||||||||||||||||||
3次元再構成 | 解像度: 3.84 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 82684 / 対称性のタイプ: POINT | ||||||||||||||||||||||||||||||||||||||||
原子モデル構築 | 空間: REAL 詳細: Starting models: 60S ribosomal subunit, tRNAs and nascent chain from 6om0. Sec61 heterotrimer from 6fti. Nicalin, TMEM147 are iTasser homology models based on 5a63. TMCO1 and CCDC47 are co- ...詳細: Starting models: 60S ribosomal subunit, tRNAs and nascent chain from 6om0. Sec61 heterotrimer from 6fti. Nicalin, TMEM147 are iTasser homology models based on 5a63. TMCO1 and CCDC47 are co-evolution-based models from RaptorX-Contact. | ||||||||||||||||||||||||||||||||||||||||
原子モデル構築 |
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