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データを開く
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基本情報
登録情報 | ![]() | |||||||||
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タイトル | Structure of the human 48S initiation complex in open state (h48S AUG open) | |||||||||
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![]() | 48S / initiation / eIF3 / ternary complex / translation / open state / RIBOSOME | |||||||||
機能・相同性 | ![]() male germ cell proliferation / positive regulation of mRNA binding / translation initiation ternary complex / regulation of translation in response to endoplasmic reticulum stress / glial limiting end-foot / HRI-mediated signaling / viral translational termination-reinitiation / Cellular response to mitochondrial stress / response to manganese-induced endoplasmic reticulum stress / positive regulation of type B pancreatic cell apoptotic process ...male germ cell proliferation / positive regulation of mRNA binding / translation initiation ternary complex / regulation of translation in response to endoplasmic reticulum stress / glial limiting end-foot / HRI-mediated signaling / viral translational termination-reinitiation / Cellular response to mitochondrial stress / response to manganese-induced endoplasmic reticulum stress / positive regulation of type B pancreatic cell apoptotic process / eukaryotic translation initiation factor 3 complex, eIF3e / Response of EIF2AK1 (HRI) to heme deficiency / Recycling of eIF2:GDP / negative regulation of translational initiation in response to stress / cap-dependent translational initiation / methionyl-initiator methionine tRNA binding / eukaryotic translation initiation factor 3 complex, eIF3m / PERK-mediated unfolded protein response / PERK regulates gene expression / IRES-dependent viral translational initiation / response to kainic acid / translation reinitiation / eukaryotic translation initiation factor 2 complex / eukaryotic translation initiation factor 3 complex / formation of cytoplasmic translation initiation complex / cytoplasmic translational initiation / multi-eIF complex / regulation of translational initiation in response to stress / eukaryotic 43S preinitiation complex / translation factor activity, RNA binding / mRNA cap binding / formation of translation preinitiation complex / eukaryotic 48S preinitiation complex / oxidized pyrimidine DNA binding / response to TNF agonist / negative regulation of endoplasmic reticulum unfolded protein response / positive regulation of base-excision repair / positive regulation of respiratory burst involved in inflammatory response / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of gastrulation / protein tyrosine kinase inhibitor activity / IRE1-RACK1-PP2A complex / positive regulation of endodeoxyribonuclease activity / nucleolus organization / positive regulation of Golgi to plasma membrane protein transport / TNFR1-mediated ceramide production / negative regulation of DNA repair / negative regulation of RNA splicing / metal-dependent deubiquitinase activity / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / supercoiled DNA binding / neural crest cell differentiation / protein-synthesizing GTPase / NF-kappaB complex / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / cysteine-type endopeptidase activator activity involved in apoptotic process / positive regulation of ubiquitin-protein transferase activity / regulation of translational initiation / oxidized purine DNA binding / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / negative regulation of bicellular tight junction assembly / ubiquitin-like protein conjugating enzyme binding / regulation of establishment of cell polarity / negative regulation of phagocytosis / rRNA modification in the nucleus and cytosol / Formation of the ternary complex, and subsequently, the 43S complex / erythrocyte homeostasis / cytoplasmic side of rough endoplasmic reticulum membrane / laminin receptor activity / negative regulation of ubiquitin protein ligase activity / protein kinase A binding / ion channel inhibitor activity / Ribosomal scanning and start codon recognition / pigmentation / Translation initiation complex formation / positive regulation of mitochondrial depolarization / positive regulation of T cell receptor signaling pathway / fibroblast growth factor binding / negative regulation of Wnt signaling pathway / monocyte chemotaxis / positive regulation of activated T cell proliferation / negative regulation of translational frameshifting / Protein hydroxylation / TOR signaling / BH3 domain binding / SARS-CoV-1 modulates host translation machinery / regulation of cell division / cellular response to ethanol / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / mTORC1-mediated signalling / iron-sulfur cluster binding / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal small subunit binding / Eukaryotic Translation Termination / ubiquitin ligase inhibitor activity / positive regulation of GTPase activity / Response of EIF2AK4 (GCN2) to amino acid deficiency 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: 4.7 Å | |||||||||
![]() | Yi S-H / Petrychenko V / Schliep JE / Goyal A / Linden A / Chari A / Urlaub H / Stark H / Rodnina MV / Adio S / Fischer N | |||||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Conformational rearrangements upon start codon recognition in human 48S translation initiation complex. 著者: Sung-Hui Yi / Valentyn Petrychenko / Jan Erik Schliep / Akanksha Goyal / Andreas Linden / Ashwin Chari / Henning Urlaub / Holger Stark / Marina V Rodnina / Sarah Adio / Niels Fischer / ![]() 要旨: Selection of the translation start codon is a key step during protein synthesis in human cells. We obtained cryo-EM structures of human 48S initiation complexes and characterized the intermediates of ...Selection of the translation start codon is a key step during protein synthesis in human cells. We obtained cryo-EM structures of human 48S initiation complexes and characterized the intermediates of codon recognition by kinetic methods using eIF1A as a reporter. Both approaches capture two distinct ribosome populations formed on an mRNA with a cognate AUG codon in the presence of eIF1, eIF1A, eIF2-GTP-Met-tRNAiMet and eIF3. The 'open' 40S subunit conformation differs from the human 48S scanning complex and represents an intermediate preceding the codon recognition step. The 'closed' form is similar to reported structures of complexes from yeast and mammals formed upon codon recognition, except for the orientation of eIF1A, which is unique in our structure. Kinetic experiments show how various initiation factors mediate the population distribution of open and closed conformations until 60S subunit docking. Our results provide insights into the timing and structure of human translation initiation intermediates and suggest the differences in the mechanisms of start codon selection between mammals and yeast. | |||||||||
履歴 |
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構造の表示
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 | ![]() | 162.4 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 77.4 KB 77.4 KB | 表示 表示 | ![]() |
FSC (解像度算出) | ![]() | 12.8 KB | 表示 | ![]() |
画像 | ![]() | 119.2 KB | ||
マスクデータ | ![]() | 178 MB | ![]() | |
Filedesc metadata | ![]() | 18.3 KB | ||
その他 | ![]() ![]() | 140.7 MB 140.7 MB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-検証レポート
文書・要旨 | ![]() | 957 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 956.5 KB | 表示 | |
XML形式データ | ![]() | 20.5 KB | 表示 | |
CIF形式データ | ![]() | 26.9 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
関連構造データ | ![]() 7qp6MC ![]() 7qp7C M: このマップから作成された原子モデル C: 同じ文献を引用 ( |
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類似構造データ | 類似検索 - 機能・相同性 ![]() |
電子顕微鏡画像生データ | ![]() Data size: 1.1 TB Data #1: Motion-corrected, dose-weighted micrographs [micrographs - single frame] Data #2: Particles of human 48S IC in open state ("open") [picked particles - single frame - processed] Data #3: Particles of human 48S IC in closed state ("closed") [picked particles - single frame - processed]) |
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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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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: 1.16 Å | ||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
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-添付データ
-マスク #1
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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_14113_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: #2
ファイル | emd_14113_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 |
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試料の構成要素
+全体 : Human 48S initiation complex 40S-eIF1-eIF1A-eIF2-eIF3-tRNA-Met-mRNA
+超分子 #1: Human 48S initiation complex 40S-eIF1-eIF1A-eIF2-eIF3-tRNA-Met-mRNA
+分子 #1: Eukaryotic translation initiation factor 3 subunit B
+分子 #2: Eukaryotic translation initiation factor 3 subunit K
+分子 #3: Eukaryotic translation initiation factor 3 subunit F
+分子 #4: Eukaryotic translation initiation factor 3 subunit L
+分子 #5: Eukaryotic translation initiation factor 3 subunit M
+分子 #7: Eukaryotic translation initiation factor 3 subunit H
+分子 #8: 60S ribosomal protein L41
+分子 #10: 40S ribosomal protein S11
+分子 #11: 40S ribosomal protein S4, X isoform
+分子 #12: 40S ribosomal protein S9
+分子 #13: 40S ribosomal protein S23
+分子 #14: 40S ribosomal protein S30
+分子 #15: 40S ribosomal protein S7
+分子 #16: 40S ribosomal protein S27
+分子 #17: 40S ribosomal protein S13
+分子 #18: 40S ribosomal protein S15a
+分子 #19: 40S ribosomal protein S21
+分子 #20: 40S ribosomal protein S2
+分子 #21: 40S ribosomal protein S17
+分子 #22: 40S ribosomal protein SA
+分子 #23: 40S ribosomal protein S3a
+分子 #24: 40S ribosomal protein S14
+分子 #25: 40S ribosomal protein S26
+分子 #26: 40S ribosomal protein S8
+分子 #27: 40S ribosomal protein S6
+分子 #28: 40S ribosomal protein S24
+分子 #29: 40S ribosomal protein S5
+分子 #30: 40S ribosomal protein S16
+分子 #31: 40S ribosomal protein S3
+分子 #32: 40S ribosomal protein S10
+分子 #33: 40S ribosomal protein S15
+分子 #34: Receptor of activated protein C kinase 1
+分子 #35: 40S ribosomal protein S19
+分子 #36: 40S ribosomal protein S25
+分子 #37: 40S ribosomal protein S18
+分子 #38: 40S ribosomal protein S20
+分子 #39: 40S ribosomal protein S29
+分子 #40: Ubiquitin-40S ribosomal protein S27a
+分子 #41: 40S ribosomal protein S12
+分子 #42: 40S ribosomal protein S28
+分子 #43: Eukaryotic translation initiation factor 3 subunit G
+分子 #44: Eukaryotic translation initiation factor 1
+分子 #45: Eukaryotic translation initiation factor 1A, X-chromosomal
+分子 #46: Eukaryotic translation initiation factor 2 subunit 1
+分子 #47: Eukaryotic translation initiation factor 2 subunit 2
+分子 #48: Eukaryotic translation initiation factor 2 subunit 3
+分子 #49: Eukaryotic translation initiation factor 3 subunit A
+分子 #50: Eukaryotic translation initiation factor 3 subunit E
+分子 #52: Eukaryotic translation initiation factor 3 subunit D
+分子 #53: Eukaryotic translation initiation factor 3 subunit C
+分子 #6: mRNA
+分子 #9: 18S rRNA
+分子 #51: Initiator Met-tRNA-i
+分子 #54: ZINC ION
+分子 #55: MAGNESIUM ION
-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
緩衝液 | pH: 7.5 詳細: 20 mM Hepes, pH 7.5, 95 mM KOAc, 3.75 mM Mg(OAc)2, 1 mM ATP, 0.5 mM GTP, 0.25 mM spermidine, 2 mM DTT, 0.4 U/uL RiboLock RNase inhibitor |
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グリッド | モデル: Quantifoil R3.5/1 / 材質: COPPER / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: CONTINUOUS |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 277 K / 装置: FEI VITROBOT MARK IV 詳細: Cryo-EM grids were prepared by floating home-made continuous carbon on 40 ul sample in the wells of teflon block (custom-made). The sample-covered carbon was then adsorbed to an EM grid.. |
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電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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詳細 | Aberration corrections performed using Cs image corrector (CEOS company) |
撮影 | フィルム・検出器のモデル: FEI FALCON III (4k x 4k) 検出モード: INTEGRATING / デジタル化 - サイズ - 横: 4096 pixel / デジタル化 - サイズ - 縦: 4096 pixel / 撮影したグリッド数: 1 / 実像数: 15544 / 平均露光時間: 1.0 sec. / 平均電子線量: 48.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: ![]() |
電子光学系 | 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 0.01 mm / 最大 デフォーカス(公称値): 4.0 µm / 最小 デフォーカス(公称値): 1.5 µm / 倍率(公称値): 59000 |
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 |