+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-21435 | |||||||||
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タイトル | Single Particle Cryo-EM Structure of the Natively Isolated Sec61, TMCO1, Nicalin, TMEM147, and CCDC47 Containing Ribosome-Translocon Complex After Focused Refinement with Local Angular Searches | |||||||||
マップデータ | ||||||||||
試料 |
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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 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.8 Å | |||||||||
データ登録者 | McGilvray PT / Anghel SA / Sundaram A / Trnka MJ / Zhong F / Hu H / Burlingame AL / Keenan RJ | |||||||||
資金援助 | 米国, 1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 | 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_21435.map.gz | 412.1 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-21435-v30.xml emd-21435.xml | 66.1 KB 66.1 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_21435_fsc.xml | 17.6 KB | 表示 | FSCデータファイル |
画像 | emd_21435.png | 140.8 KB | ||
マスクデータ | emd_21435_msk_1.map | 476.8 MB | マスクマップ | |
その他 | emd_21435_half_map_1.map.gz emd_21435_half_map_2.map.gz | 416.1 MB 416.8 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-21435 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21435 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_21435_validation.pdf.gz | 516.9 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_21435_full_validation.pdf.gz | 516.5 KB | 表示 | |
XML形式データ | emd_21435_validation.xml.gz | 22.7 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21435 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21435 | 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_21435.map.gz / 形式: CCP4 / 大きさ: 476.8 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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: 1.36 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
-マスク #1
ファイル | emd_21435_msk_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: #2
ファイル | emd_21435_half_map_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: #1
ファイル | emd_21435_half_map_2.map | ||||||||||||
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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 : Native complex of a translating ribosome and a novel translocon c...
+超分子 #1: Native complex of a translating ribosome and a novel translocon c...
+超分子 #2: 60S Subunit
+超分子 #3: 40S Subunit
+超分子 #4: Translocon
+超分子 #5: Sec61 Complex
+超分子 #6: TMCO1
+超分子 #7: NOMO-Nicalin-TMEM147 Complex
+超分子 #8: CCDC47
+超分子 #9: 60S acidic ribosomal protein P0
+超分子 #10: 60S acidic ribosomal protein P1
+超分子 #11: 60S acidic ribosomal protein P2
+超分子 #12: 60S ribosomal protein L10
+超分子 #13: 60S ribosomal protein L10a
+超分子 #14: 60S ribosomal protein L11
+超分子 #15: 60S ribosomal protein L12
+超分子 #16: 60S ribosomal protein L13
+超分子 #17: 60S ribosomal protein L13a
+超分子 #18: 60S ribosomal protein L14
+超分子 #19: 60S ribosomal protein L15
+超分子 #20: 60S ribosomal protein L17
+超分子 #21: 60S ribosomal protein L18
+超分子 #22: 60S ribosomal protein L18a
+超分子 #23: 60S ribosomal protein L19
+超分子 #24: 60S ribosomal protein L21
+超分子 #25: 60S ribosomal protein L22
+超分子 #26: 60S ribosomal protein L23
+超分子 #27: 60S ribosomal protein L23a
+超分子 #28: 60S ribosomal protein L24
+超分子 #29: 60S ribosomal protein L26
+超分子 #30: 60S ribosomal protein L27
+超分子 #31: 60S ribosomal protein L27a
+超分子 #32: 60S ribosomal protein L28
+超分子 #33: 60S ribosomal protein L3
+超分子 #34: 60S ribosomal protein L30
+超分子 #35: 60S ribosomal protein L31
+超分子 #36: 60S ribosomal protein L32
+超分子 #37: 60S ribosomal protein L34
+超分子 #38: 60S ribosomal protein L35
+超分子 #39: 60S ribosomal protein L35a
+超分子 #40: 60S ribosomal protein L36
+超分子 #41: 60S ribosomal protein L36a
+超分子 #42: 60S ribosomal protein L37a
+超分子 #43: 60S ribosomal protein L38
+超分子 #44: 60S ribosomal protein L39
+超分子 #45: 60S ribosomal protein L4
+超分子 #46: 60S ribosomal protein L5
+超分子 #47: 60S ribosomal protein L6
+超分子 #48: 60S ribosomal protein L7
+超分子 #49: 60S ribosomal protein L7a
+超分子 #50: 60S ribosomal protein L8
+超分子 #51: 60S ribosomal protein L9
+超分子 #52: 40S ribosomal protein S10
+超分子 #53: 40S ribosomal protein S11
+超分子 #54: 40S ribosomal protein S12
+超分子 #55: 40S ribosomal protein S13
+超分子 #56: 40S ribosomal protein S14
+超分子 #57: 40S ribosomal protein S15
+超分子 #58: 40S ribosomal protein S15a
+超分子 #59: 40S ribosomal protein S16
+超分子 #60: 40S ribosomal protein S17
+超分子 #61: 40S ribosomal protein S18
+超分子 #62: 40S ribosomal protein S19
+超分子 #63: 40S ribosomal protein S2
+超分子 #64: 40S ribosomal protein S20
+超分子 #65: 40S ribosomal protein S21
+超分子 #66: 40S ribosomal protein S23
+超分子 #67: 40S ribosomal protein S24
+超分子 #68: 40S ribosomal protein S25
+超分子 #69: 40S ribosomal protein S26
+超分子 #70: 40S ribosomal protein S27
+超分子 #71: 40S ribosomal protein S27-like
+超分子 #72: 40S ribosomal protein S28
+超分子 #73: 40S ribosomal protein S29
+超分子 #74: 40S ribosomal protein S3
+超分子 #75: 40S ribosomal protein S30
+超分子 #76: 40S ribosomal protein S3a
+超分子 #77: 40S ribosomal protein S4, X isoform
+超分子 #78: 40S ribosomal protein S5
+超分子 #79: 40S ribosomal protein S6
+超分子 #80: 40S ribosomal protein S7
+超分子 #81: 40S ribosomal protein S8
+超分子 #82: 40S ribosomal protein S9
+超分子 #83: 40S ribosomal protein SA
-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
濃度 | 0.4 mg/mL | |||||||||||||||
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緩衝液 | pH: 7.4 構成要素:
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グリッド | モデル: C-flat-1.2/1.3 / 材質: COPPER / メッシュ: 200 / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: CONTINUOUS / 支持フィルム - Film thickness: 2.0 nm / 前処理 - タイプ: GLOW DISCHARGE / 詳細: unspecified | |||||||||||||||
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 298 K / 装置: FEI VITROBOT MARK IV 詳細: Two filter papers were added to each arm, 2.5 microliters of sample were added to grids, and 0.5 second of drain time was allowed before vitrification.. | |||||||||||||||
詳細 | Sample was well-dispersed on a thin (~2nm) carbon film. |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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撮影 | #0 - Image recording ID: 1 #0 - フィルム・検出器のモデル: GATAN K3 (6k x 4k) #0 - 検出モード: COUNTING / #0 - 撮影したグリッド数: 1 / #0 - 実像数: 5562 / #0 - 平均露光時間: 3.8 sec. / #0 - 平均電子線量: 50.0 e/Å2 / #1 - Image recording ID: 2 #1 - フィルム・検出器のモデル: GATAN K3 (6k x 4k) #1 - 撮影したグリッド数: 1 / #1 - 実像数: 5562 / #1 - 平均露光時間: 3.8 sec. / #1 - 平均電子線量: 50.0 e/Å2 |
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: FLOOD BEAM / 撮影モード: BRIGHT FIELD |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |