+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-10760 | |||||||||
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タイトル | Mammalian 48S late-stage initiation complex with beta-globin 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 / ribosomal small subunit binding ...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 / ribosomal small subunit binding / 90S preribosome / TOR signaling / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / T cell proliferation involved in immune response / regulation of translational fidelity / erythrocyte development / ribosomal subunit export from nucleus / ribosomal small subunit export from nucleus / translation regulator activity / translational termination / 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 / cytosolic ribosome / translation initiation factor activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rescue of stalled ribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / cellular response to leukemia inhibitory factor / small-subunit processome / translational initiation / protein kinase C binding / positive regulation of apoptotic signaling pathway / positive regulation of protein-containing complex assembly / placenta development / spindle / cytoplasmic stress granule / cytoplasmic ribonucleoprotein granule / modification-dependent protein catabolic process / G1/S transition of mitotic cell cycle / rRNA processing / protein tag activity / ribosomal small subunit biogenesis / rhythmic process / positive regulation of canonical Wnt signaling pathway / small ribosomal subunit rRNA binding / ribosome binding / glucose homeostasis / regulation of translation / ribosomal small subunit assembly / virus receptor activity / small ribosomal subunit / T cell differentiation in thymus / cell body / cytosolic small ribosomal subunit / perikaryon / cytoplasmic translation / cytosolic large ribosomal subunit / mitochondrial inner membrane / cell differentiation / postsynaptic density / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / iron ion binding / positive regulation of apoptotic process / ribonucleoprotein complex / positive regulation of protein phosphorylation / translation / cell division / DNA repair / mRNA binding / centrosome / ubiquitin protein ligase binding / dendrite / positive regulation of cell population proliferation / synapse / negative regulation of apoptotic process / nucleolus / apoptotic process / protein kinase binding / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / ATP hydrolysis activity / DNA binding / RNA binding / zinc ion binding / ATP binding / membrane / nucleus / metal ion binding / plasma membrane / cytosol 類似検索 - 分子機能 | |||||||||
生物種 | Oryctolagus cuniculus (ウサギ) / Homo sapiens (ヒト) / 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: 3.0 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_10760.map.gz | 202.6 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-10760-v30.xml emd-10760.xml | 55.4 KB 55.4 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_10760.png | 151.8 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-10760 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10760 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_10760_validation.pdf.gz | 304.8 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_10760_full_validation.pdf.gz | 303.9 KB | 表示 | |
XML形式データ | emd_10760_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-10760 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10760 | 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_10760.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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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: 1.1 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 beta-globin mRNA
+超分子 #1: LS48S IC with beta-globin mRNA
+超分子 #2: LS48S IC
+超分子 #3: beta-globin mRNA
+分子 #1: initiator methionylated tRNA
+分子 #34: 18S ribosomal RNA
+分子 #41: beta-globin mRNA
+分子 #2: 60s ribosomal protein ul41
+分子 #3: 40S ribosomal protein uS2
+分子 #4: 40S ribosomal protein eS1
+分子 #5: 40S ribosomal protein uS5
+分子 #6: 40S Ribosomal protein uS3
+分子 #7: 40S ribosomal protein eS4
+分子 #8: 40S Ribosomal protein uS7
+分子 #9: 40S ribosomal protein eS6
+分子 #10: 40S ribosomal protein eS7
+分子 #11: 40S ribosomal protein eS8
+分子 #12: 40S ribosomal protein uS4
+分子 #13: 40S ribosomal protein eS10
+分子 #14: 40S ribosomal protein uS17
+分子 #15: 40S ribosomal protein eS12
+分子 #16: 40S ribosomal protein uS15
+分子 #17: 40S ribosomal protein uS11
+分子 #18: 40S ribosomal protein uS9
+分子 #19: 40S ribosomal protein eS17
+分子 #20: 40S ribosomal protein eS19
+分子 #21: 40S ribosomal protein uS10
+分子 #22: 40S ribosomal protein eS21
+分子 #23: 40S ribosomal protein uS8
+分子 #24: 40S ribosomal protein uS12
+分子 #25: 40S ribosomal protein eS24
+分子 #26: 40S ribosomal protein eS26
+分子 #27: 40S ribosomal protein eS27
+分子 #28: 40S ribosomal protein eS28
+分子 #29: 40S ribosomal protein uS14
+分子 #30: 40S ribosomal protein eS31
+分子 #31: ribosomal protein RACK1
+分子 #32: 40S ribosomal protein eS25
+分子 #33: 40S ribosomal protein eS30
+分子 #35: Eukaryotic translation initiation factor 2 subunit alpha
+分子 #36: Eukaryotic translation initiation factor 2 subunit gamma
+分子 #37: eukaryotic translation initiation factor 1A
+分子 #38: ATP-binding cassette sub-family E member 1 (ABCE1)
+分子 #39: 40S ribosomal protein uS13
+分子 #40: 40S ribosomal protein uS19
+分子 #42: IRON/SULFUR CLUSTER
+分子 #43: MAGNESIUM ION
+分子 #44: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
-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 / チャンバー内湿度: 100 % |
-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: 3.0 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 252000 |
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-6yal: |