+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-10762 | |||||||||
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タイトル | Mammalian 48S late-stage translation initiation complex with histone 4 mRNA | |||||||||
マップデータ | ||||||||||
試料 |
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機能・相同性 | 機能・相同性情報 eukaryotic translation initiation factor 2 complex / ribosomal subunit / eukaryotic 48S preinitiation complex / laminin receptor activity / mammalian oogenesis stage / activation-induced cell death of T cells / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / phagocytic cup / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) ...eukaryotic translation initiation factor 2 complex / ribosomal subunit / eukaryotic 48S preinitiation complex / laminin receptor activity / mammalian oogenesis stage / activation-induced cell death of T cells / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / phagocytic cup / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / TOR signaling / T cell proliferation involved in immune response / ribosomal small subunit export from nucleus / erythrocyte development / translation regulator activity / cytosolic ribosome / laminin binding / rough endoplasmic reticulum / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / gastrulation / MDM2/MDM4 family protein binding / translation initiation factor activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / rescue of stalled ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cellular response to leukemia inhibitory factor / maturation of SSU-rRNA / small-subunit processome / positive regulation of apoptotic signaling pathway / protein kinase C binding / positive regulation of protein-containing complex assembly / placenta development / cytoplasmic ribonucleoprotein granule / cytoplasmic stress granule / modification-dependent protein catabolic process / spindle / G1/S transition of mitotic cell cycle / rRNA processing / protein tag activity / rhythmic process / positive regulation of canonical Wnt signaling pathway / ribosome binding / glucose homeostasis / virus receptor activity / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cell body / T cell differentiation in thymus / perikaryon / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / mitochondrial inner membrane / cytoplasmic translation / postsynaptic density / cell differentiation / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / ribonucleoprotein complex / translation / positive regulation of protein phosphorylation / positive regulation of apoptotic process / cell cycle / cell division / DNA repair / centrosome / mRNA binding / apoptotic process / ubiquitin protein ligase binding / synapse / dendrite / positive regulation of cell population proliferation / nucleolus / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / DNA binding / RNA binding / zinc ion binding / membrane / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol 類似検索 - 分子機能 | |||||||||
生物種 | Oryctolagus cuniculus (ウサギ) / Mus musculus (ハツカネズミ) / Rabbit (ウサギ) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.48 Å | |||||||||
データ登録者 | Bochler A / Simonetti A / Guca E / Hashem Y | |||||||||
資金援助 | European Union, フランス, 2件
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引用 | ジャーナル: Cell Rep / 年: 2020 タイトル: Structural Insights into the Mammalian Late-Stage Initiation Complexes. 著者: Angelita Simonetti / Ewelina Guca / Anthony Bochler / Lauriane Kuhn / Yaser Hashem / 要旨: In higher eukaryotes, the mRNA sequence in the direct vicinity of the start codon, called the Kozak sequence (CRCCaugG, where R is a purine), is known to influence the rate of the initiation process. ...In higher eukaryotes, the mRNA sequence in the direct vicinity of the start codon, called the Kozak sequence (CRCCaugG, where R is a purine), is known to influence the rate of the initiation process. However, the molecular basis underlying its role remains poorly understood. Here, we present the cryoelectron microscopy (cryo-EM) structures of mammalian late-stage 48S initiation complexes (LS48S ICs) in the presence of two different native mRNA sequences, β-globin and histone 4, at overall resolution of 3 and 3.5 Å, respectively. Our high-resolution structures unravel key interactions from the mRNA to eukaryotic initiation factors (eIFs): 1A, 2, 3, 18S rRNA, and several 40S ribosomal proteins. In addition, we are able to study the structural role of ABCE1 in the formation of native 48S ICs. Our results reveal a comprehensive map of ribosome/eIF-mRNA and ribosome/eIF-tRNA interactions and suggest the impact of mRNA sequence on the structure of the LS48S IC. | |||||||||
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_10762.map.gz | 18.2 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-10762-v30.xml emd-10762.xml | 51.5 KB 51.5 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_10762.png | 152.1 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-10762 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10762 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_10762_validation.pdf.gz | 240.8 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_10762_full_validation.pdf.gz | 240 KB | 表示 | |
XML形式データ | emd_10762_validation.xml.gz | 6.8 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10762 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10762 | 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_10762.map.gz / 形式: CCP4 / 大きさ: 216 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: 1.1 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
-試料の構成要素
+全体 : LS48S IC with histone 4 mRNA
+超分子 #1: LS48S IC with histone 4 mRNA
+超分子 #2: LS48S IC
+超分子 #3: histone 4 mRNA
+分子 #1: 60s ribosomal protein l41
+分子 #2: 40S ribosomal protein SA
+分子 #3: ribosomal protein eS1
+分子 #4: 40S ribosomal protein uS5
+分子 #5: Ribosomal protein S3
+分子 #6: 40S ribosomal protein S4
+分子 #7: Ribosomal protein S5
+分子 #8: 40S ribosomal protein S6
+分子 #9: ribosomal protein eS7
+分子 #10: 40S ribosomal protein S8
+分子 #11: Ribosomal protein S9 (Predicted)
+分子 #12: 40S ribosomal protein eS10
+分子 #13: Ribosomal protein S11
+分子 #14: 40S ribosomal protein S12
+分子 #15: ribosomal protein uS15
+分子 #16: 40S ribosomal protein uS11
+分子 #17: ribosomal protein uS9
+分子 #18: ribosomal protein eS17
+分子 #19: 40S ribosomal protein eS19
+分子 #20: Ribosomal_S10 domain-containing protein
+分子 #21: 40S ribosomal protein S21
+分子 #22: Ribosomal protein S15a
+分子 #23: 40S ribosomal protein uS12
+分子 #24: 40S ribosomal protein S24
+分子 #25: 40S ribosomal protein eS26
+分子 #26: 40S ribosomal protein S27
+分子 #27: ribosomal protein eS28
+分子 #28: ribosomal protein uS14
+分子 #29: ribosomal protein eS31
+分子 #30: ribosomal protein RACK1
+分子 #31: ribosomal protein eS25
+分子 #32: 40S ribosomal protein eS30
+分子 #35: Eukaryotic translation initiation factor 2 subunit 1
+分子 #36: eukaryotic translation initiation factor 2 subunit gamma
+分子 #37: 40S ribosomal protein uS13
+分子 #38: Ribosomal protein S15
+分子 #33: 18S ribosomal RNA
+分子 #34: histone 4 (H4) mRNA
+分子 #39: initiator methionylated tRNA
-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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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 SUMMIT (4k x 4k) 検出モード: SUPER-RESOLUTION / 平均電子線量: 26.0 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 |
-画像解析
初期モデル | モデルのタイプ: PDB ENTRY PDBモデル - PDB ID: |
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最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 3.48 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 372000 |
初期 角度割当 | タイプ: PROJECTION MATCHING |
最終 角度割当 | タイプ: PROJECTION MATCHING |
-原子モデル構築 1
精密化 | プロトコル: FLEXIBLE FIT |
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得られたモデル | PDB-6yan: |