+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-17700 | |||||||||
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タイトル | Structure of human 48S translation initiation complex after eIF2 release prior 60S subunit joining (48S-5) | |||||||||
マップデータ | ||||||||||
試料 |
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キーワード | RIBOSOME / TRANSLATION / initiation / 48S / eIF / human / eukaryotic / factor / codon / scanning / closed | |||||||||
機能・相同性 | 機能・相同性情報 positive regulation of mRNA binding / viral translational termination-reinitiation / eukaryotic translation initiation factor 3 complex, eIF3e / cap-dependent translational initiation / eukaryotic translation initiation factor 3 complex, eIF3m / translation reinitiation / IRES-dependent viral translational initiation / multi-eIF complex / formation of cytoplasmic translation initiation complex / eukaryotic translation initiation factor 3 complex ...positive regulation of mRNA binding / viral translational termination-reinitiation / eukaryotic translation initiation factor 3 complex, eIF3e / cap-dependent translational initiation / eukaryotic translation initiation factor 3 complex, eIF3m / translation reinitiation / IRES-dependent viral translational initiation / multi-eIF complex / formation of cytoplasmic translation initiation complex / eukaryotic translation initiation factor 3 complex / protein-synthesizing GTPase / eukaryotic 43S preinitiation complex / cytoplasmic translational initiation / translation factor activity, RNA binding / mRNA cap binding / positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / eukaryotic 48S preinitiation complex / protein tyrosine kinase inhibitor activity / positive regulation of respiratory burst involved in inflammatory response / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of gastrulation / nucleolus organization / 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 DNA repair / negative regulation of RNA splicing / metal-dependent deubiquitinase activity / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / oxidized purine DNA binding / supercoiled 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 / negative regulation of phagocytosis / positive regulation of ubiquitin-protein transferase activity / 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 / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / 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 / pigmentation / mammalian oogenesis stage / positive regulation of mitochondrial depolarization / activation-induced cell death of T cells / positive regulation of T cell receptor signaling pathway / negative regulation of Wnt signaling pathway / fibroblast growth factor binding / positive regulation of activated T cell proliferation / iron-sulfur cluster binding / regulation of cell division / Protein hydroxylation / negative regulation of peptidyl-serine phosphorylation / BH3 domain binding / mTORC1-mediated signalling / SARS-CoV-1 modulates host translation machinery / monocyte chemotaxis / Peptide chain elongation / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / cysteine-type endopeptidase activator activity involved in apoptotic process / Selenocysteine synthesis / positive regulation of signal transduction by p53 class mediator / Formation of a pool of free 40S subunits / phagocytic cup / Eukaryotic Translation Termination / ubiquitin ligase inhibitor activity / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / negative regulation of respiratory burst involved in inflammatory response / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / L13a-mediated translational silencing of Ceruloplasmin expression / TOR signaling / T cell proliferation involved in immune response / spindle assembly / Major pathway of rRNA processing in the nucleolus and cytosol / regulation of translational fidelity / erythrocyte development / Protein methylation / negative regulation of ubiquitin-dependent protein catabolic process / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / translation regulator activity 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: 2.9 Å | |||||||||
データ登録者 | Petrychenko V / Yi S-H / Liedtke D / Peng BZ / Rodnina MV / Fischer N | |||||||||
資金援助 | ドイツ, 2件
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引用 | ジャーナル: Nat.Struct.Mol.Biol. / 年: 2024 タイトル: Structural basis for translational control by the human 48S initiation complex from codon scanning toward subunit joining 著者: Petrychenko V / Yi S-H / Liedtke D / Peng BZ / Rodnina MV / Fischer N | |||||||||
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 | emd_17700.map.gz | 272.6 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-17700-v30.xml emd-17700.xml | 83.6 KB 83.6 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_17700_fsc.xml | 12.7 KB | 表示 | FSCデータファイル |
画像 | emd_17700.png | 162.4 KB | ||
マスクデータ | emd_17700_msk_1.map | 178 MB | マスクマップ | |
Filedesc metadata | emd-17700.cif.gz | 18.8 KB | ||
その他 | emd_17700_additional_1.map.gz emd_17700_additional_2.map.gz emd_17700_additional_3.map.gz emd_17700_additional_4.map.gz emd_17700_half_map_1.map.gz emd_17700_half_map_2.map.gz | 140.6 MB 140.3 MB 140.8 MB 163 MB 140.5 MB 140.5 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-17700 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17700 | HTTPS FTP |
-関連構造データ
関連構造データ | 8pj5MC 17696 17697 17698 17699 17701 19128 8pj1C 8pj2C 8pj3C 8pj4C 8pj6C 8rg0C 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 (文献) |
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類似構造データ | 類似検索 - 機能・相同性F&H 検索 |
-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_17700.map.gz / 形式: CCP4 / 大きさ: 307.5 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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ボクセルのサイズ | X=Y=Z: 0.967 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
ファイル | emd_17700_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 |
-試料の構成要素
+全体 : Human 48S initiation complex 40S-eIF1A-eIF3-eIF5-eIF5B-tRNA-Met-mRNA
+超分子 #1: Human 48S initiation complex 40S-eIF1A-eIF3-eIF5-eIF5B-tRNA-Met-mRNA
+分子 #1: Eukaryotic translation initiation factor 5B
+分子 #2: Eukaryotic translation initiation factor 3 subunit B
+分子 #3: Eukaryotic translation initiation factor 3 subunit I
+分子 #4: Eukaryotic translation initiation factor 3 subunit K
+分子 #5: Eukaryotic translation initiation factor 3 subunit F
+分子 #6: Eukaryotic translation initiation factor 3 subunit L
+分子 #7: Eukaryotic translation initiation factor 3 subunit M
+分子 #9: Eukaryotic translation initiation factor 3 subunit H
+分子 #10: 60S ribosomal protein L41
+分子 #12: 40S ribosomal protein S11
+分子 #13: 40S ribosomal protein S4, X isoform
+分子 #14: 40S ribosomal protein S9
+分子 #15: 40S ribosomal protein S23
+分子 #16: 40S ribosomal protein S30
+分子 #17: 40S ribosomal protein S7
+分子 #18: 40S ribosomal protein S27
+分子 #19: 40S ribosomal protein S13
+分子 #20: 40S ribosomal protein S15a
+分子 #21: 40S ribosomal protein S21
+分子 #22: 40S ribosomal protein S2
+分子 #23: 40S ribosomal protein S17
+分子 #24: 40S ribosomal protein SA
+分子 #25: 40S ribosomal protein S3a
+分子 #26: 40S ribosomal protein S14
+分子 #27: 40S ribosomal protein S26
+分子 #28: 40S ribosomal protein S8
+分子 #29: 40S ribosomal protein S6
+分子 #30: 40S ribosomal protein S24
+分子 #31: 40S ribosomal protein S5
+分子 #32: 40S ribosomal protein S16
+分子 #33: 40S ribosomal protein S3
+分子 #34: 40S ribosomal protein S10
+分子 #35: 40S ribosomal protein S15
+分子 #36: Receptor of activated protein C kinase 1
+分子 #37: 40S ribosomal protein S19
+分子 #38: 40S ribosomal protein S25
+分子 #39: 40S ribosomal protein S18
+分子 #40: 40S ribosomal protein S20
+分子 #41: 40S ribosomal protein S29
+分子 #42: Ubiquitin
+分子 #43: 40S ribosomal protein S12
+分子 #44: 40S ribosomal protein S28
+分子 #45: Eukaryotic translation initiation factor 3 subunit G
+分子 #46: Eukaryotic translation initiation factor 1A, X-chromosomal
+分子 #47: Eukaryotic translation initiation factor 3 subunit A
+分子 #48: Eukaryotic translation initiation factor 3 subunit E
+分子 #50: Eukaryotic translation initiation factor 3 subunit D
+分子 #51: Eukaryotic translation initiation factor 3 subunit C
+分子 #8: mRNA
+分子 #11: 18S rRNA
+分子 #49: Initiator Met-tRNA-i
+分子 #52: MAGNESIUM ION
+分子 #53: GUANOSINE-5'-TRIPHOSPHATE
+分子 #54: ZINC 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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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: 7.5 構成要素:
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凍結 | 凍結剤: ETHANE / 装置: HOMEMADE PLUNGER / 詳細: Manual blotting & plunge-freezing. |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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特殊光学系 | 球面収差補正装置: Electron-optical aberrations were corrected using a CETCOR Cs-corrector (CEOS, Heidelberg) aligned with the CETCORPLUS 4.6.9 software package (CEOS, Heidelberg). |
撮影 | フィルム・検出器のモデル: FEI FALCON III (4k x 4k) 平均露光時間: 1.5 sec. / 平均電子線量: 45.0 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: SPOT SCAN / 撮影モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 2.5 µm / 最小 デフォーカス(公称値): 0.2 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 |