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万見- EMDB-11458: Structure of a human ABCE1-bound 43S pre-initiation complex - State II -
+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-11458 | |||||||||
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タイトル | Structure of a human ABCE1-bound 43S pre-initiation complex - State II | |||||||||
マップデータ | ||||||||||
試料 |
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キーワード | Translation / Initiation / Ribosome Recycling / ABC Proteins / RIBOSOME | |||||||||
機能・相同性 | 機能・相同性情報 negative regulation of endoribonuclease activity / CTPase activity / positive regulation of mRNA binding / positive regulation of mRNA cis splicing, via spliceosome / viral translational termination-reinitiation / eukaryotic translation initiation factor 3 complex, eIF3e / cap-dependent translational initiation / eukaryotic translation initiation factor 3 complex, eIF3m / IRES-dependent viral translational initiation / translation reinitiation ...negative regulation of endoribonuclease activity / CTPase activity / positive regulation of mRNA binding / positive regulation of mRNA cis splicing, via spliceosome / viral translational termination-reinitiation / eukaryotic translation initiation factor 3 complex, eIF3e / cap-dependent translational initiation / eukaryotic translation initiation factor 3 complex, eIF3m / IRES-dependent viral translational initiation / translation reinitiation / OAS antiviral response / eukaryotic translation initiation factor 3 complex / formation of cytoplasmic translation initiation complex / multi-eIF complex / cytoplasmic translational initiation / translation factor activity, RNA binding / mRNA cap binding / eukaryotic 43S preinitiation complex / ribosome disassembly / : / ribosomal subunit / negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / protein tyrosine kinase inhibitor activity / positive regulation of respiratory burst involved in inflammatory response / eukaryotic 48S preinitiation complex / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of gastrulation / nucleolus organization / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / IRE1-RACK1-PP2A complex / positive regulation of endodeoxyribonuclease activity / positive regulation of Golgi to plasma membrane protein transport / TNFR1-mediated ceramide production / negative regulation of RNA splicing / negative regulation of DNA repair / metal-dependent deubiquitinase activity / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / supercoiled DNA binding / oxidized purine DNA binding / neural crest cell differentiation / NF-kappaB complex / ubiquitin-like protein conjugating enzyme binding / regulation of translational initiation / regulation of establishment of cell polarity / positive regulation of ubiquitin-protein transferase activity / negative regulation of phagocytosis / rRNA modification in the nucleus and cytosol / erythrocyte homeostasis / Formation of the ternary complex, and subsequently, the 43S complex / cytoplasmic side of rough endoplasmic reticulum membrane / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / laminin receptor activity / pigmentation / protein kinase A binding / negative regulation of ubiquitin protein ligase activity / Ribosomal scanning and start codon recognition / ion channel inhibitor activity / Translation initiation complex formation / mammalian oogenesis stage / fibroblast growth factor binding / positive regulation of mitochondrial depolarization / activation-induced cell death of T cells / positive regulation of T cell receptor signaling pathway / negative regulation of peptidyl-serine phosphorylation / iron-sulfur cluster binding / negative regulation of Wnt signaling pathway / positive regulation of activated T cell proliferation / monocyte chemotaxis / Protein hydroxylation / regulation of cell division / BH3 domain binding / cysteine-type endopeptidase activator activity involved in apoptotic process / mTORC1-mediated signalling / SARS-CoV-1 modulates host translation machinery / Peptide chain elongation / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Selenocysteine synthesis / positive regulation of signal transduction by p53 class mediator / Formation of a pool of free 40S subunits / ubiquitin ligase inhibitor activity / Eukaryotic Translation Termination / phagocytic cup / ribosomal small subunit binding / negative regulation of respiratory burst involved in inflammatory response / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / endoribonuclease inhibitor activity / L13a-mediated translational silencing of Ceruloplasmin expression / TOR signaling / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / T cell proliferation involved in immune response / regulation of translational fidelity / spindle assembly 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 | Kratzat H / Mackens-Kiani T | |||||||||
資金援助 | ドイツ, フランス, 2件
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引用 | ジャーナル: EMBO J / 年: 2021 タイトル: A structural inventory of native ribosomal ABCE1-43S pre-initiation complexes. 著者: Hanna Kratzat / Timur Mackens-Kiani / Michael Ameismeier / Mia Potocnjak / Jingdong Cheng / Estelle Dacheux / Abdelkader Namane / Otto Berninghausen / Franz Herzog / Micheline Fromont-Racine ...著者: Hanna Kratzat / Timur Mackens-Kiani / Michael Ameismeier / Mia Potocnjak / Jingdong Cheng / Estelle Dacheux / Abdelkader Namane / Otto Berninghausen / Franz Herzog / Micheline Fromont-Racine / Thomas Becker / Roland Beckmann / 要旨: In eukaryotic translation, termination and ribosome recycling phases are linked to subsequent initiation of a new round of translation by persistence of several factors at ribosomal sub-complexes. ...In eukaryotic translation, termination and ribosome recycling phases are linked to subsequent initiation of a new round of translation by persistence of several factors at ribosomal sub-complexes. These comprise/include the large eIF3 complex, eIF3j (Hcr1 in yeast) and the ATP-binding cassette protein ABCE1 (Rli1 in yeast). The ATPase is mainly active as a recycling factor, but it can remain bound to the dissociated 40S subunit until formation of the next 43S pre-initiation complexes. However, its functional role and native architectural context remains largely enigmatic. Here, we present an architectural inventory of native yeast and human ABCE1-containing pre-initiation complexes by cryo-EM. We found that ABCE1 was mostly associated with early 43S, but also with later 48S phases of initiation. It adopted a novel hybrid conformation of its nucleotide-binding domains, while interacting with the N-terminus of eIF3j. Further, eIF3j occupied the mRNA entry channel via its ultimate C-terminus providing a structural explanation for its antagonistic role with respect to mRNA binding. Overall, the native human samples provide a near-complete molecular picture of the architecture and sophisticated interaction network of the 43S-bound eIF3 complex and the eIF2 ternary complex containing the initiator tRNA. | |||||||||
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_11458.map.gz | 194 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-11458-v30.xml emd-11458.xml | 78.7 KB 78.7 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_11458_fsc.xml | 14.2 KB | 表示 | FSCデータファイル |
画像 | emd_11458.png | 193.8 KB | ||
Filedesc metadata | emd-11458.cif.gz | 15.4 KB | ||
その他 | emd_11458_additional_1.map.gz emd_11458_additional_2.map.gz emd_11458_additional_3.map.gz emd_11458_additional_4.map.gz emd_11458_additional_5.map.gz emd_11458_additional_6.map.gz emd_11458_additional_7.map.gz | 25.7 MB 140 MB 19.5 MB 15.2 MB 14.4 MB 3.3 MB 3 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-11458 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11458 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_11458_validation.pdf.gz | 752.8 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_11458_full_validation.pdf.gz | 752.4 KB | 表示 | |
XML形式データ | emd_11458_validation.xml.gz | 14.1 KB | 表示 | |
CIF形式データ | emd_11458_validation.cif.gz | 19.1 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11458 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11458 | 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_11458.map.gz / 形式: CCP4 / 大きさ: 244.1 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: 1.059 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: post processed and masked map
ファイル | emd_11458_additional_1.map | ||||||||||||
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注釈 | post processed and masked map | ||||||||||||
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密度ヒストグラム |
-追加マップ: local resolution filtered map
ファイル | emd_11458_additional_2.map | ||||||||||||
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注釈 | local resolution filtered map | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: multi body refinement body 1
ファイル | emd_11458_additional_3.map | ||||||||||||
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注釈 | multi body refinement body 1 | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: multi body refinement body 2
ファイル | emd_11458_additional_4.map | ||||||||||||
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注釈 | multi body refinement body 2 | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: multi body refinement body 3
ファイル | emd_11458_additional_5.map | ||||||||||||
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注釈 | multi body refinement body 3 | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: multi body refinement if eIF3 core body 1
ファイル | emd_11458_additional_6.map | ||||||||||||
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注釈 | multi body refinement if eIF3 core body 1 | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: multi body refinement if eIF3 core body 2
ファイル | emd_11458_additional_7.map | ||||||||||||
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注釈 | multi body refinement if eIF3 core body 2 | ||||||||||||
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 : ABCE1-bound 43S initiation complex
+超分子 #1: ABCE1-bound 43S initiation complex
+分子 #1: 40S ribosomal protein SA
+分子 #2: 40S ribosomal protein S3a
+分子 #3: 40S ribosomal protein S2
+分子 #4: 40S ribosomal protein S26
+分子 #5: 40S ribosomal protein S4, X isoform
+分子 #6: 60S ribosomal protein L41
+分子 #7: 40S ribosomal protein S6
+分子 #8: 40S ribosomal protein S7
+分子 #9: 40S ribosomal protein S8
+分子 #10: 40S ribosomal protein S9
+分子 #11: 40S ribosomal protein S11
+分子 #12: 40S ribosomal protein S13
+分子 #13: 40S ribosomal protein S14
+分子 #14: 40S ribosomal protein S21
+分子 #15: 40S ribosomal protein S15a
+分子 #16: 40S ribosomal protein S23
+分子 #17: 40S ribosomal protein S24
+分子 #18: 40S ribosomal protein S27
+分子 #19: 40S ribosomal protein S30
+分子 #21: 40S ribosomal protein S17
+分子 #22: 40S ribosomal protein S16
+分子 #23: 40S ribosomal protein S3
+分子 #24: 40S ribosomal protein S5
+分子 #25: 40S ribosomal protein S10
+分子 #26: 40S ribosomal protein S12
+分子 #27: 40S ribosomal protein S15
+分子 #28: 40S ribosomal protein S18
+分子 #29: 40S ribosomal protein S19
+分子 #30: 40S ribosomal protein S20
+分子 #31: 40S ribosomal protein S25
+分子 #32: 40S ribosomal protein S28
+分子 #33: 40S ribosomal protein S29
+分子 #34: Ubiquitin-40S ribosomal protein S27a
+分子 #35: Receptor of activated protein C kinase 1
+分子 #36: Eukaryotic translation initiation factor 3 subunit I
+分子 #37: Eukaryotic translation initiation factor 3 subunit B
+分子 #38: Eukaryotic translation initiation factor 3 subunit A
+分子 #39: Eukaryotic translation initiation factor 3 subunit C
+分子 #40: Eukaryotic translation initiation factor 3 subunit E
+分子 #41: Eukaryotic translation initiation factor 3 subunit F
+分子 #42: Eukaryotic translation initiation factor 3 subunit H
+分子 #43: Eukaryotic translation initiation factor 3 subunit K
+分子 #44: Eukaryotic translation initiation factor 3 subunit L
+分子 #45: Eukaryotic translation initiation factor 3 subunit M
+分子 #46: ATP-binding cassette sub-family E member 1
+分子 #47: Eukaryotic translation initiation factor 1
+分子 #48: Eukaryotic translation initiation factor 3 subunit D
+分子 #49: RNA recognition motif (unknown)
+分子 #50: Eukaryotic translation initiation factor 3 subunit J
+分子 #20: 18S ribosomal RNA
+分子 #51: ZINC ION
+分子 #52: IRON/SULFUR CLUSTER
+分子 #53: ADENOSINE-5'-DIPHOSPHATE
+分子 #54: MAGNESIUM ION
+分子 #55: ADENOSINE-5'-TRIPHOSPHATE
-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
緩衝液 | pH: 7.6 |
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凍結 | 凍結剤: ETHANE |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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撮影 | フィルム・検出器のモデル: GATAN K2 QUANTUM (4k x 4k) 平均電子線量: 48.0 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 |