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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 human 48S translation initiation complex after eIF5 release (48S-4) | |||||||||
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![]() | RIBOSOME / TRANSLATION / initiation / 48S / eIF / human / eukaryotic / factor / codon / scanning / closed | |||||||||
機能・相同性 | ![]() 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 ...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 / translation factor activity, RNA binding / eukaryotic 43S preinitiation complex / mRNA cap binding / formation of translation preinitiation complex / eukaryotic 48S preinitiation complex / negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / response to TNF agonist / 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 / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / 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 RNA splicing / negative regulation of DNA repair / metal-dependent deubiquitinase activity / protein-synthesizing GTPase / supercoiled DNA binding / neural crest cell differentiation / positive regulation of ubiquitin-protein transferase activity / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / NF-kappaB complex / cysteine-type endopeptidase activator activity involved in apoptotic process / 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 / regulation of establishment of cell polarity / ubiquitin-like protein conjugating enzyme binding / negative regulation of phagocytosis / Formation of the ternary complex, and subsequently, the 43S complex / rRNA modification in the nucleus and cytosol / erythrocyte homeostasis / cytoplasmic side of rough endoplasmic reticulum membrane / laminin receptor activity / negative regulation of ubiquitin protein ligase activity / ion channel inhibitor activity / protein kinase A binding / 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 / positive regulation of activated T cell proliferation / monocyte chemotaxis / 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 / mTORC1-mediated signalling / iron-sulfur cluster binding / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ubiquitin ligase inhibitor activity / Eukaryotic Translation Termination / positive regulation of signal transduction by p53 class mediator / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / negative regulation of ubiquitin-dependent protein catabolic process 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: 3.2 Å | |||||||||
![]() | Petrychenko V / Yi S-H / Liedtke D / Peng BZ / Rodnina MV / Fischer N | |||||||||
資金援助 | ![]()
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![]() | ジャーナル: Protein Sci / 年: 2018 タイトル: UCSF ChimeraX: Meeting modern challenges in visualization and analysis. 著者: Thomas D Goddard / Conrad C Huang / Elaine C Meng / Eric F Pettersen / Gregory S Couch / John H Morris / Thomas E Ferrin / ![]() 要旨: UCSF ChimeraX is next-generation software for the visualization and analysis of molecular structures, density maps, 3D microscopy, and associated data. It addresses challenges in the size, scope, and ...UCSF ChimeraX is next-generation software for the visualization and analysis of molecular structures, density maps, 3D microscopy, and associated data. It addresses challenges in the size, scope, and disparate types of data attendant with cutting-edge experimental methods, while providing advanced options for high-quality rendering (interactive ambient occlusion, reliable molecular surface calculations, etc.) and professional approaches to software design and distribution. This article highlights some specific advances in the areas of visualization and usability, performance, and extensibility. ChimeraX is free for noncommercial use and is available from http://www.rbvi.ucsf.edu/chimerax/ for Windows, Mac, and Linux. | |||||||||
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 | ![]() | 275 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 86.1 KB 86.1 KB | 表示 表示 | ![]() |
FSC (解像度算出) | ![]() | 12.7 KB | 表示 | ![]() |
画像 | ![]() | 187.7 KB | ||
マスクデータ | ![]() | 178 MB | ![]() | |
Filedesc metadata | ![]() | 20.1 KB | ||
その他 | ![]() ![]() ![]() ![]() ![]() | 163.4 MB 162.4 MB 140.6 MB 140.7 MB 140.9 MB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-検証レポート
文書・要旨 | ![]() | 1 MB | 表示 | ![]() |
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文書・詳細版 | ![]() | 1 MB | 表示 | |
XML形式データ | ![]() | 21.9 KB | 表示 | |
CIF形式データ | ![]() | 27.8 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 | ![]() 8pj4MC ![]() 8pj1C ![]() 8pj2C ![]() 8pj3C ![]() 8pj5C ![]() 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 ( |
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類似構造データ | 類似検索 - 機能・相同性 ![]() |
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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: 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 | ![]() | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-追加マップ: eIF2-GDP substate 1 (48S-4-1)
ファイル | emd_17699_additional_1.map | ||||||||||||
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注釈 | eIF2-GDP substate 1 (48S-4-1) | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: eIF2-GDP substate 2 (48S-4-2)
ファイル | emd_17699_additional_2.map | ||||||||||||
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注釈 | eIF2-GDP substate 2 (48S-4-2) | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: Unsharpened main map from 3D refinement step
ファイル | emd_17699_additional_3.map | ||||||||||||
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注釈 | Unsharpened main map from 3D refinement step | ||||||||||||
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_17699_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_17699_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-eIF1A-eIF2-eIF3-eIF5B-tRNA-Met-mRNA
+超分子 #1: Human 48S initiation complex 40S-eIF1A-eIF2-eIF3-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: Small ribosomal subunit protein eS30
+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 2 subunit 1
+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 #8: mRNA
+分子 #11: 18S rRNA
+分子 #51: Initiator Met-tRNA-i
+分子 #54: GUANOSINE-5'-TRIPHOSPHATE
+分子 #55: SODIUM ION
+分子 #56: MAGNESIUM ION
+分子 #57: 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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![]() | 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 構成要素:
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凍結 | 凍結剤: ETHANE / 装置: HOMEMADE PLUNGER / 詳細: Manual blotting & plunge-freezing. |
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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: ![]() |
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 |