+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-17297 | ||||||||||||
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タイトル | Structure of a human 48S translation initiation complex with eIF4F and eIF4A | ||||||||||||
マップデータ | Human 48S complex | ||||||||||||
試料 |
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キーワード | translation / eIF4A / eIF4F / initiation / ribosome / mRNA | ||||||||||||
機能・相同性 | 機能・相同性情報 positive regulation of eukaryotic translation initiation factor 4F complex assembly / positive regulation of mRNA cap binding / eukaryotic initiation factor eIF2 binding / male germ cell proliferation / positive regulation of mRNA binding / regulation of translation in response to endoplasmic reticulum stress / translation initiation ternary complex / glial limiting end-foot / response to kainic acid / positive regulation of translation in response to endoplasmic reticulum stress ...positive regulation of eukaryotic translation initiation factor 4F complex assembly / positive regulation of mRNA cap binding / eukaryotic initiation factor eIF2 binding / male germ cell proliferation / positive regulation of mRNA binding / regulation of translation in response to endoplasmic reticulum stress / translation initiation ternary complex / glial limiting end-foot / response to kainic acid / positive regulation of translation in response to endoplasmic reticulum stress / HRI-mediated signaling / Cellular response to mitochondrial stress / viral translational termination-reinitiation / response to manganese-induced endoplasmic reticulum stress / macromolecule biosynthetic process / positive regulation of type B pancreatic cell apoptotic process / methionyl-initiator methionine tRNA binding / eukaryotic translation initiation factor 3 complex, eIF3e / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / negative regulation of translational initiation in response to stress / Response of EIF2AK1 (HRI) to heme deficiency / cap-dependent translational initiation / regulation of cellular response to stress / eukaryotic translation initiation factor 3 complex, eIF3m / Recycling of eIF2:GDP / PERK-mediated unfolded protein response / eukaryotic initiation factor 4E binding / translation reinitiation / PERK regulates gene expression / eukaryotic translation initiation factor 2 complex / IRES-dependent viral translational initiation / regulation of translational initiation in response to stress / RNA cap binding / multi-eIF complex / formation of cytoplasmic translation initiation complex / eukaryotic translation initiation factor 3 complex / eukaryotic translation initiation factor 4F complex / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / protein-synthesizing GTPase / eukaryotic 43S preinitiation complex / cytoplasmic translational initiation / translation factor activity, RNA binding / mRNA cap binding / formation of translation preinitiation complex / Deadenylation of mRNA / miRNA-mediated gene silencing by inhibition of translation / 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 / M-decay: degradation of maternal mRNAs by maternally stored factors / 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 / positive regulation of protein localization to cell periphery / 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 / GDP-dissociation inhibitor activity / 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 / positive regulation of mitochondrial depolarization / mammalian oogenesis stage / activation-induced cell death of T cells / negative regulation of Wnt signaling pathway / positive regulation of T cell receptor signaling pathway / negative regulation of peptidyl-threonine phosphorylation / fibroblast growth factor binding / positive regulation of activated T cell proliferation / iron-sulfur cluster binding / regulation of cell division 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: 3.5 Å | ||||||||||||
データ登録者 | Brito Querido J / Sokabe M / Diaz-Lopez I / Gordiyenko Y / Fraser CS / Ramakrishnan V | ||||||||||||
資金援助 | 英国, 米国, 3件
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引用 | ジャーナル: Nat Struct Mol Biol / 年: 2024 タイトル: The structure of a human translation initiation complex reveals two independent roles for the helicase eIF4A. 著者: Jailson Brito Querido / Masaaki Sokabe / Irene Díaz-López / Yuliya Gordiyenko / Christopher S Fraser / V Ramakrishnan / 要旨: Eukaryotic translation initiation involves recruitment of the 43S pre-initiation complex to the 5' end of mRNA by the cap-binding complex eIF4F, forming the 48S translation initiation complex (48S), ...Eukaryotic translation initiation involves recruitment of the 43S pre-initiation complex to the 5' end of mRNA by the cap-binding complex eIF4F, forming the 48S translation initiation complex (48S), which then scans along the mRNA until the start codon is recognized. We have previously shown that eIF4F binds near the mRNA exit channel of the 43S, leaving open the question of how mRNA secondary structure is removed as it enters the mRNA channel on the other side of the 40S subunit. Here we report the structure of a human 48S that shows that, in addition to the eIF4A that is part of eIF4F, there is a second eIF4A helicase bound at the mRNA entry site, which could unwind RNA secondary structures as they enter the 48S. The structure also reveals conserved interactions between eIF4F and the 43S, probaby explaining how eIF4F can promote mRNA recruitment in all eukaryotes. | ||||||||||||
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_17297.map.gz | 32.6 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-17297-v30.xml emd-17297.xml | 108.8 KB 108.8 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_17297_fsc.xml | 14.2 KB | 表示 | FSCデータファイル |
画像 | emd_17297.png | 85.4 KB | ||
マスクデータ | emd_17297_msk_1.map | 244.1 MB | マスクマップ | |
Filedesc metadata | emd-17297.cif.gz | 20.8 KB | ||
その他 | emd_17297_additional_1.map.gz emd_17297_additional_10.map.gz emd_17297_additional_11.map.gz emd_17297_additional_2.map.gz emd_17297_additional_3.map.gz emd_17297_additional_4.map.gz emd_17297_additional_5.map.gz emd_17297_additional_6.map.gz emd_17297_additional_7.map.gz emd_17297_additional_8.map.gz emd_17297_additional_9.map.gz emd_17297_half_map_1.map.gz emd_17297_half_map_2.map.gz | 190.3 MB 13 MB 209.8 MB 152.6 MB 144.3 MB 209.3 MB 139.3 MB 5.1 MB 3.4 MB 192.5 MB 8.6 MB 194.6 MB 193.8 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-17297 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17297 | HTTPS FTP |
-関連構造データ
関連構造データ | 8oz0MC 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_17297.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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注釈 | Human 48S complex | ||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.06 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
+追加マップ: Body1 - 3D multi-body refinement of 48S
+追加マップ: eIF3 after focus 4F
+追加マップ: PIC after focus EntrySite
+追加マップ: Body2 - 3D multi-body refinement of 48S
+追加マップ: Body3 - 3D multi-body refinement of 48S
+追加マップ: PIC after focus EntrySite Resampled map
+追加マップ: eIF4F-eIF3 after focus EntrySite Resampled map
+追加マップ: eIF3 after focus 4F Resampled map
+追加マップ: eIF4F after focus 4F Resampled map
+追加マップ: eIF4F eIF3 after focus 4F
+追加マップ: eIF4F after focus 4F
+ハーフマップ: Half map1 48S
+ハーフマップ: Half map1 48S
-試料の構成要素
+全体 : Human 48S translation initiation complex
+超分子 #1: Human 48S translation initiation complex
+分子 #1: Eukaryotic translation initiation factor 3 subunit E
+分子 #2: Eukaryotic translation initiation factor 3 subunit F
+分子 #3: Eukaryotic translation initiation factor 3 subunit G
+分子 #4: Eukaryotic translation initiation factor 3 subunit H
+分子 #5: 60S ribosomal protein L41
+分子 #6: Eukaryotic translation initiation factor 3 subunit A
+分子 #7: Eukaryotic translation initiation factor 3 subunit K
+分子 #8: Eukaryotic translation initiation factor 3 subunit M
+分子 #9: Eukaryotic translation initiation factor 2 subunit 1
+分子 #10: Eukaryotic translation initiation factor 2 subunit 3
+分子 #11: Eukaryotic translation initiation factor 3 subunit I
+分子 #12: Eukaryotic translation initiation factor 1A, X-chromosomal
+分子 #13: Eukaryotic translation initiation factor 5
+分子 #14: Eukaryotic translation initiation factor 3 subunit B
+分子 #15: Eukaryotic translation initiation factor 3 subunit C
+分子 #16: Eukaryotic translation initiation factor 3 subunit L
+分子 #17: 40S ribosomal protein S7
+分子 #18: 40S ribosomal protein S27
+分子 #19: 40S ribosomal protein S21
+分子 #20: 40S ribosomal protein S2
+分子 #21: 40S ribosomal protein S3a
+分子 #22: 40S ribosomal protein SA
+分子 #23: 40S ribosomal protein S26
+分子 #24: 40S ribosomal protein S6
+分子 #25: 40S ribosomal protein S14
+分子 #26: Eukaryotic translation initiation factor 2 subunit 2
+分子 #27: 40S ribosomal protein S13
+分子 #29: 40S ribosomal protein S11
+分子 #30: 40S ribosomal protein S4, X isoform
+分子 #31: 40S ribosomal protein S9
+分子 #32: 40S ribosomal protein S23
+分子 #33: 40S ribosomal protein S30
+分子 #34: 40S ribosomal protein S15a
+分子 #35: 40S ribosomal protein S8
+分子 #36: 40S ribosomal protein S24
+分子 #37: 40S ribosomal protein S5
+分子 #38: 40S ribosomal protein S16
+分子 #39: 40S ribosomal protein S3
+分子 #40: 40S ribosomal protein S10
+分子 #41: 40S ribosomal protein S15
+分子 #42: Receptor of activated protein C kinase 1
+分子 #43: 40S ribosomal protein S19
+分子 #44: 40S ribosomal protein S25
+分子 #45: Small ribosomal subunit protein uS13
+分子 #46: 40S ribosomal protein S29
+分子 #47: Ubiquitin-40S ribosomal protein S27a
+分子 #48: 40S ribosomal protein S12
+分子 #49: 40S ribosomal protein S28
+分子 #50: 40S ribosomal protein S17
+分子 #51: 40S ribosomal protein S20
+分子 #52: Eukaryotic translation initiation factor 3 subunit D
+分子 #55: Eukaryotic initiation factor 4A-I
+分子 #56: Eukaryotic translation initiation factor 4 gamma 1
+分子 #28: 18S rRNA
+分子 #53: tRNAiMet
+分子 #54: mRNA
+分子 #57: ZINC ION
+分子 #58: 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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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: 7.4 |
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グリッド | モデル: UltrAuFoil R1.2/1.3 / 支持フィルム - 材質: GRAPHENE OXIDE / 前処理 - タイプ: GLOW DISCHARGE |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 277.15 K |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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ソフトウェア | 名称: EPU |
撮影 | フィルム・検出器のモデル: GATAN K3 (6k x 4k) / 平均電子線量: 47.88 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: OTHER / 撮影モード: OTHER / 最大 デフォーカス(公称値): 3.0 µm / 最小 デフォーカス(公称値): 1.2 µm |
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 |